rs1960997

Variant names:

• chr11-97772824-T-C
• rs1960997

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.145 in 152,168 control chromosomes in the GnomAD database, including 1,809 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 0.14 (1809 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.31
• Publications: 3 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.283 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: 0.145 AC: 21996 AN: 152050 Hom.: 1804 Cov.: 32

Gnomad AFR AF: 0.118

Gnomad AMI AF: 0.129

Gnomad AMR AF: 0.143

Gnomad ASJ AF: 0.201

Gnomad EAS AF: 0.295

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.161

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.141

Gnomad OTH AF: 0.152

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

GnomAD4 genome AF: 0.145 AC: 22019 AN: 152168 Hom.: 1809 Cov.: 32 AF XY: 0.148 AC XY: 10999 AN XY: 74384

African (AFR) AF: 0.118 AC: 4882 AN: 41534

American (AMR) AF: 0.143 AC: 2185 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.201 AC: 699 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1527 AN: 5174

South Asian (SAS) AF: 0.192 AC: 927 AN: 4822

European-Finnish (FIN) AF: 0.161 AC: 1700 AN: 10568

Middle Eastern (MID) AF: 0.204 AC: 60 AN: 294

European-Non Finnish (NFE) AF: 0.141 AC: 9592 AN: 67996

Other (OTH) AF: 0.156 AC: 329 AN: 2110

Alfa AF: 0.144 Hom.: 882

Bravo AF: 0.139

Asia WGS AF: 0.241 AC: 836 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	15
DANN	Benign	0.82
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs1960997; hg19: chr11-97643824;