rs2297939

chr6-111227959-G-Achr6-111227959-G-C

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC16A10	NM_018593.5	c.*5724G>A		3_prime_UTR_variant	6/6	ENST00000368851.10
MFSD4B-DT	XR_001743807.2	n.175-36C>T		intron_variant, non_coding_transcript_variant
MFSD4B-DT	XR_001743806.2	n.218-36C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SLC16A10	ENST00000368851.10	c.*5724G>A		3_prime_UTR_variant	6/6	1	NM_018593.5	P1
SLC16A10	ENST00000368850.4	c.*5724G>A		3_prime_UTR_variant	5/5	1
MFSD4B-DT	ENST00000425364.1	n.257-36C>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 NFE exome AF: 0.500

Gnomad4 OTH exome AF: 0.500

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

Gnomad4 AFR AF: 0.0915

Gnomad4 AMR AF: 0.353

Gnomad4 ASJ AF: 0.417

Gnomad4 EAS AF: 0.418

Gnomad4 SAS AF: 0.446

Gnomad4 FIN AF: 0.363

Gnomad4 NFE AF: 0.414

Gnomad4 OTH AF: 0.337

Alfa AF: 0.393 Hom.: 14287

Bravo AF: 0.306

Asia WGS AF: 0.379 AC: 1317 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	0.35
Dann	Benign	0.45

Splicing

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

Publications

LitVar

Other links and lift over

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