rs7772697

Variant names:

• chr6-149113975-T-C
• rs7772697
• ENST00000834740.1:n.229-39421A>G

Variant summary

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

The ENST00000834740.1(ENSG00000308521):​n.229-39421A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.428 in 151,938 control chromosomes in the GnomAD database, including 14,487 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 0.43 (14487 hom., cov: 32)
• Consequence: ENSG00000308521 ENST00000834740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0450
• Publications: 14 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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.503 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.229-39421A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.428 AC: 65022 AN: 151820 Hom.: 14466 Cov.: 32

Gnomad AFR AF: 0.509

Gnomad AMI AF: 0.466

Gnomad AMR AF: 0.296

Gnomad ASJ AF: 0.305

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.436

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.380

Gnomad NFE AF: 0.424

Gnomad OTH AF: 0.399

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

GnomAD4 genome AF: 0.428 AC: 65092 AN: 151938 Hom.: 14487 Cov.: 32 AF XY: 0.429 AC XY: 31834 AN XY: 74242

African (AFR) AF: 0.509 AC: 21078 AN: 41408

American (AMR) AF: 0.296 AC: 4520 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.305 AC: 1060 AN: 3470

East Asian (EAS) AF: 0.188 AC: 968 AN: 5154

South Asian (SAS) AF: 0.435 AC: 2090 AN: 4808

European-Finnish (FIN) AF: 0.489 AC: 5153 AN: 10544

Middle Eastern (MID) AF: 0.388 AC: 114 AN: 294

European-Non Finnish (NFE) AF: 0.424 AC: 28838 AN: 67964

Other (OTH) AF: 0.402 AC: 846 AN: 2104

Alfa AF: 0.415 Hom.: 55673

Bravo AF: 0.411

Asia WGS AF: 0.413 AC: 1434 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.2
DANN	Benign	0.34
PhyloP100		-0.045

Splicing

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

Other links and lift over

dbSNP: rs7772697; hg19: chr6-149435111;