rs6837311

Variant names:

• chr4-99274116-T-A
• rs6837311
• ENST00000500358.6:n.3790-12679T>A

Variant summary

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

The ENST00000500358.6(ENSG00000246090):​n.3790-12679T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.274 in 152,208 control chromosomes in the GnomAD database, including 7,056 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 0.27 (7056 hom., cov: 33)
  • Exomes 𝑓: 0.50 (0 hom.)
• Consequence: ENSG00000246090 ENST00000500358.6 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0950
• Publications: 9 publications found

Genes affected

ENSG00000246090 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.382 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100507053	NR_037884.1	n.3790-12679T>A		intron_variant	Intron 4 of 9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000246090	ENST00000500358.6	n.3790-12679T>A		intron_variant	Intron 4 of 9	1
ENSG00000246090	ENST00000509295.5	n.695-9T>A		intron_variant	Intron 4 of 5	1
ENSG00000246090	ENST00000757833.1	n.104T>A		non_coding_transcript_exon_variant	Exon 1 of 6

Frequencies

GnomAD3 genomes AF: 0.275 AC: 41770 AN: 152088 Hom.: 7060 Cov.: 33

Gnomad AFR AF: 0.100

Gnomad AMI AF: 0.470

Gnomad AMR AF: 0.263

Gnomad ASJ AF: 0.462

Gnomad EAS AF: 0.0261

Gnomad SAS AF: 0.155

Gnomad FIN AF: 0.345

Gnomad MID AF: 0.369

Gnomad NFE AF: 0.386

Gnomad OTH AF: 0.330

GnomAD4 exome AF: 0.500 AC: 1 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.500 AC XY: 1 AN XY: 2

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) AC: 0 AN: 0

GnomAD4 genome AF: 0.274 AC: 41773 AN: 152206 Hom.: 7056 Cov.: 33 AF XY: 0.268 AC XY: 19921 AN XY: 74410

African (AFR) AF: 0.100 AC: 4168 AN: 41544

American (AMR) AF: 0.263 AC: 4020 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.462 AC: 1603 AN: 3468

East Asian (EAS) AF: 0.0262 AC: 136 AN: 5194

South Asian (SAS) AF: 0.157 AC: 757 AN: 4832

European-Finnish (FIN) AF: 0.345 AC: 3646 AN: 10566

Middle Eastern (MID) AF: 0.356 AC: 104 AN: 292

European-Non Finnish (NFE) AF: 0.386 AC: 26223 AN: 68002

Other (OTH) AF: 0.327 AC: 690 AN: 2112

Alfa AF: 0.328 Hom.: 1117

Bravo AF: 0.260

Asia WGS AF: 0.0990 AC: 348 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	4.9
DANN	Benign	0.44
PhyloP100		-0.095

Splicing

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

Other links and lift over

dbSNP: rs6837311; hg19: chr4-100195273;