rs11210892

Variant names:

• chr1-43634413-G-A
• rs11210892

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 0.511 in 151,942 control chromosomes in the GnomAD database, including 23,539 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 0.51 (23539 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 58 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.673 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: 0.511 AC: 77596 AN: 151824 Hom.: 23531 Cov.: 32

Gnomad AFR AF: 0.175

Gnomad AMI AF: 0.687

Gnomad AMR AF: 0.493

Gnomad ASJ AF: 0.641

Gnomad EAS AF: 0.693

Gnomad SAS AF: 0.459

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.676

Gnomad OTH AF: 0.554

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

GnomAD4 genome AF: 0.511 AC: 77634 AN: 151942 Hom.: 23539 Cov.: 32 AF XY: 0.508 AC XY: 37734 AN XY: 74278

African (AFR) AF: 0.175 AC: 7262 AN: 41418

American (AMR) AF: 0.493 AC: 7520 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.641 AC: 2219 AN: 3464

East Asian (EAS) AF: 0.692 AC: 3575 AN: 5164

South Asian (SAS) AF: 0.460 AC: 2212 AN: 4812

European-Finnish (FIN) AF: 0.658 AC: 6940 AN: 10552

Middle Eastern (MID) AF: 0.568 AC: 166 AN: 292

European-Non Finnish (NFE) AF: 0.676 AC: 45939 AN: 67972

Other (OTH) AF: 0.559 AC: 1176 AN: 2104

Alfa AF: 0.628 Hom.: 59431

Bravo AF: 0.487

Asia WGS AF: 0.559 AC: 1946 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.2
DANN	Benign	0.67
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs11210892; hg19: chr1-44100084;