rs1963605

Variant names:

• chr1-196853038-C-A
• rs1963605

Your query was ambiguous. Multiple possible variants found:

• chr1-196853038-C-A
• chr1-196853038-C-T

Variant summary

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

The variant allele was found at a frequency of 0.742 in 151,020 control chromosomes in the GnomAD database, including 42,358 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 0.74 (42358 hom., cov: 32)
• Consequence: LOC100996886 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.85
• Publications: 5 publications found

Genes affected

LOC100996886 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.779 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649395.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285986	ENST00000649395.1		n.58+2698C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.743 AC: 112063 AN: 150904 Hom.: 42347 Cov.: 32

Gnomad AFR AF: 0.720

Gnomad AMI AF: 0.863

Gnomad AMR AF: 0.665

Gnomad ASJ AF: 0.716

Gnomad EAS AF: 0.611

Gnomad SAS AF: 0.752

Gnomad FIN AF: 0.728

Gnomad MID AF: 0.896

Gnomad NFE AF: 0.784

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.742 AC: 112109 AN: 151020 Hom.: 42358 Cov.: 32 AF XY: 0.738 AC XY: 54408 AN XY: 73742

African (AFR) AF: 0.719 AC: 29354 AN: 40806

American (AMR) AF: 0.664 AC: 10066 AN: 15160

Ashkenazi Jewish (ASJ) AF: 0.716 AC: 2484 AN: 3470

East Asian (EAS) AF: 0.611 AC: 3142 AN: 5144

South Asian (SAS) AF: 0.751 AC: 3619 AN: 4822

European-Finnish (FIN) AF: 0.728 AC: 7594 AN: 10430

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.784 AC: 53230 AN: 67882

Other (OTH) AF: 0.748 AC: 1572 AN: 2102

Alfa AF: 0.708 Hom.: 2435

Bravo AF: 0.736

Asia WGS AF: 0.654 AC: 2278 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.0040
DANN	Benign	0.28
PhyloP100		-3.8
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs1963605; hg19: chr1-196822168;