rs7761698

Variant names:

• chr6-149121109-A-G
• rs7761698
• ENST00000834740.1:n.229-46555T>C

Your query was ambiguous. Multiple possible variants found:

• chr6-149121109-A-G
• chr6-149121109-A-T

Variant summary

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

The ENST00000834740.1(ENSG00000308521):​n.229-46555T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.214 in 151,954 control chromosomes in the GnomAD database, including 3,757 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 0.21 (3757 hom., cov: 32)
• Consequence: ENSG00000308521 ENST00000834740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202
• Publications: 4 publications found

Genes affected

ENSG00000308521 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.272 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308521	ENST00000834740.1	n.229-46555T>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.213 AC: 32397 AN: 151836 Hom.: 3750 Cov.: 32

Gnomad AFR AF: 0.276

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.133

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.110

Gnomad SAS AF: 0.257

Gnomad FIN AF: 0.295

Gnomad MID AF: 0.168

Gnomad NFE AF: 0.189

Gnomad OTH AF: 0.209

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.214 AC: 32451 AN: 151954 Hom.: 3757 Cov.: 32 AF XY: 0.218 AC XY: 16174 AN XY: 74244

African (AFR) AF: 0.277 AC: 11464 AN: 41458

American (AMR) AF: 0.133 AC: 2023 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 571 AN: 3468

East Asian (EAS) AF: 0.110 AC: 568 AN: 5150

South Asian (SAS) AF: 0.257 AC: 1235 AN: 4810

European-Finnish (FIN) AF: 0.295 AC: 3111 AN: 10544

Middle Eastern (MID) AF: 0.170 AC: 50 AN: 294

European-Non Finnish (NFE) AF: 0.189 AC: 12863 AN: 67956

Other (OTH) AF: 0.211 AC: 444 AN: 2108

Alfa AF: 0.193 Hom.: 9711

Bravo AF: 0.199

Asia WGS AF: 0.252 AC: 875 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.7
DANN	Benign	0.78
PhyloP100		0.20

Splicing

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

Other links and lift over

dbSNP: rs7761698; hg19: chr6-149442245;