rs970741

Variant names:

• chr1-169510807-T-C
• rs970741

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 0.256 in 151,710 control chromosomes in the GnomAD database, including 5,099 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 0.26 (5099 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.441
• Publications: 10 publications found

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 (AMR) allele frequency at 95% confidence interval = 0.339 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

Frequencies

GnomAD3 genomes AF: 0.256 AC: 38808 AN: 151592 Hom.: 5090 Cov.: 31

Gnomad AFR AF: 0.223

Gnomad AMI AF: 0.191

Gnomad AMR AF: 0.346

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.234

Gnomad SAS AF: 0.330

Gnomad FIN AF: 0.206

Gnomad MID AF: 0.253

Gnomad NFE AF: 0.266

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.256 AC: 38830 AN: 151710 Hom.: 5099 Cov.: 31 AF XY: 0.257 AC XY: 19033 AN XY: 74144

African (AFR) AF: 0.222 AC: 9202 AN: 41382

American (AMR) AF: 0.346 AC: 5262 AN: 15192

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 575 AN: 3464

East Asian (EAS) AF: 0.234 AC: 1209 AN: 5160

South Asian (SAS) AF: 0.331 AC: 1591 AN: 4808

European-Finnish (FIN) AF: 0.206 AC: 2174 AN: 10578

Middle Eastern (MID) AF: 0.245 AC: 72 AN: 294

European-Non Finnish (NFE) AF: 0.266 AC: 18009 AN: 67818

Other (OTH) AF: 0.267 AC: 562 AN: 2104

Alfa AF: 0.270 Hom.: 2968

Bravo AF: 0.266

Asia WGS AF: 0.283 AC: 982 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	1.5
DANN	Benign	0.65
PhyloP100		-0.44

Splicing

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

Other links and lift over

dbSNP: rs970741; hg19: chr1-169480045;