1-196853038-C-A

Variant names:

• chr1-196853038-C-A
• rs1963605

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC100996886		n.196853038C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285986	ENST00000649395.1	n.58+2698C>A		intron_variant	Intron 1 of 3

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 v4.3

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;