3-77901971-C-G

Variant names:

• chr3-77901971-C-G
• rs11127608
• ENST00000756757.1:n.235-35883G>C

Variant summary

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

The ENST00000756757.1(ENSG00000298601):​n.235-35883G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.346 in 151,842 control chromosomes in the GnomAD database, including 10,107 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 0.35 (10107 hom., cov: 31)
• Consequence: ENSG00000298601 ENST00000756757.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.203
• Publications: 0 publications found

Genes affected

ENSG00000298601 (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 (EAS) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377171	XR_940977.4	n.216-35883G>C		intron_variant	Intron 2 of 6
LOC105377171	XR_940978.4	n.216-35883G>C		intron_variant	Intron 2 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000298601	ENST00000756757.1	n.235-35883G>C		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756759.1	n.190-35883G>C		intron_variant	Intron 2 of 5
ENSG00000298601	ENST00000756760.1	n.221-35883G>C		intron_variant	Intron 2 of 6
ENSG00000298601	ENST00000756761.1	n.235-35883G>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52441 AN: 151726 Hom.: 10094 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.281

Gnomad EAS AF: 0.685

Gnomad SAS AF: 0.493

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.251

Gnomad OTH AF: 0.332

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

GnomAD4 genome AF: 0.346 AC: 52500 AN: 151842 Hom.: 10107 Cov.: 31 AF XY: 0.356 AC XY: 26443 AN XY: 74208

African (AFR) AF: 0.454 AC: 18785 AN: 41400

American (AMR) AF: 0.287 AC: 4389 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.281 AC: 976 AN: 3468

East Asian (EAS) AF: 0.685 AC: 3523 AN: 5144

South Asian (SAS) AF: 0.493 AC: 2371 AN: 4810

European-Finnish (FIN) AF: 0.413 AC: 4349 AN: 10538

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.251 AC: 17062 AN: 67894

Other (OTH) AF: 0.335 AC: 707 AN: 2108

Alfa AF: 0.304 Hom.: 966

Bravo AF: 0.340

Asia WGS AF: 0.574 AC: 1996 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	0.69
DANN	Benign	0.56
PhyloP100		-0.20

Splicing

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

Other links and lift over

dbSNP: rs11127608; hg19: chr3-77951122;