rs1960997

chr11-97772824-T-C

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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

Gnomad4 AFR AF: 0.118

Gnomad4 AMR AF: 0.143

Gnomad4 ASJ AF: 0.201

Gnomad4 EAS AF: 0.295

Gnomad4 SAS AF: 0.192

Gnomad4 FIN AF: 0.161

Gnomad4 NFE AF: 0.141

Gnomad4 OTH AF: 0.156

Alfa AF: 0.144 Hom.: 802

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1960997; hg19: chr11-97643824;