6-111227959-G-A

Variant names:

• chr6-111227959-G-A
• rs2297939
• NM_018593.5:c.*5724G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_018593.5(SLC16A10):​c.*5724G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.316 in 152,036 control chromosomes in the GnomAD database, including 9,126 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.32 (9126 hom., cov: 31)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: SLC16A10 NM_018593.5 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.926
• Publications: 8 publications found

Genes affected

SLC16A10 (HGNC:17027): (solute carrier family 16 member 10) SLC16A10 is a member of a family of plasma membrane amino acid transporters that mediate the Na(+)-independent transport of aromatic amino acids across the plasma membrane.[supplied by OMIM, Apr 2004]

MFSD4B-DT (HGNC:55773): (MFSD4B divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.43 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_018593.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A10	NM_018593.5	MANE Select	c.*5724G>A		3_prime_UTR	Exon 6 of 6	NP_061063.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SLC16A10	ENST00000368851.10	TSL:1 MANE Select	c.*5724G>A		3_prime_UTR	Exon 6 of 6	ENSP00000357844.4
	SLC16A10	ENST00000368850.4	TSL:1	c.*5724G>A		3_prime_UTR	Exon 5 of 5	ENSP00000357843.1
	MFSD4B-DT	ENST00000425364.2	TSL:3	n.410-36C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.316 AC: 48025 AN: 151914 Hom.: 9118 Cov.: 31

Gnomad AFR AF: 0.0917

Gnomad AMI AF: 0.341

Gnomad AMR AF: 0.352

Gnomad ASJ AF: 0.417

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.443

Gnomad FIN AF: 0.363

Gnomad MID AF: 0.386

Gnomad NFE AF: 0.414

Gnomad OTH AF: 0.341

GnomAD4 exome AF: 0.500 AC: 2 AN: 4 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AF: 0.500 AC: 1 AN: 2

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0.00000000770867), which strongly suggests a high chance of mosaicism in these individuals.

GnomAD4 genome AF: 0.316 AC: 48050 AN: 152032 Hom.: 9126 Cov.: 31 AF XY: 0.317 AC XY: 23582 AN XY: 74296

African (AFR) AF: 0.0915 AC: 3796 AN: 41484

American (AMR) AF: 0.353 AC: 5389 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.417 AC: 1449 AN: 3472

East Asian (EAS) AF: 0.418 AC: 2156 AN: 5158

South Asian (SAS) AF: 0.446 AC: 2143 AN: 4806

European-Finnish (FIN) AF: 0.363 AC: 3833 AN: 10560

Middle Eastern (MID) AF: 0.405 AC: 119 AN: 294

European-Non Finnish (NFE) AF: 0.414 AC: 28143 AN: 67962

Other (OTH) AF: 0.337 AC: 712 AN: 2112

Alfa AF: 0.383 Hom.: 17153

Bravo AF: 0.306

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.35
DANN	Benign	0.45
PhyloP100		-0.93
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2297939; hg19: chr6-111549162; COSMIC: COSV64353965; COSMIC: COSV64353965;