11-4570509-T-G

Variant names:

• chr11-4570509-T-G
• rs10768096

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 0.618 in 142,552 control chromosomes in the GnomAD database, including 27,457 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 0.62 (27457 hom., cov: 22)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.52
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.723 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: 0.618 AC: 88103 AN: 142486 Hom.: 27444 Cov.: 22

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.611

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.743

Gnomad FIN AF: 0.558

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.583

Gnomad OTH AF: 0.612

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

GnomAD4 genome AF: 0.618 AC: 88142 AN: 142552 Hom.: 27457 Cov.: 22 AF XY: 0.617 AC XY: 42475 AN XY: 68820

African (AFR) AF: 0.700 AC: 26242 AN: 37482

American (AMR) AF: 0.529 AC: 7501 AN: 14180

Ashkenazi Jewish (ASJ) AF: 0.611 AC: 2089 AN: 3418

East Asian (EAS) AF: 0.705 AC: 3341 AN: 4742

South Asian (SAS) AF: 0.744 AC: 3314 AN: 4456

European-Finnish (FIN) AF: 0.558 AC: 4886 AN: 8760

Middle Eastern (MID) AF: 0.733 AC: 198 AN: 270

European-Non Finnish (NFE) AF: 0.583 AC: 38731 AN: 66418

Other (OTH) AF: 0.614 AC: 1195 AN: 1946

Alfa AF: 0.588 Hom.: 27322

Bravo AF: 0.621

Asia WGS AF: 0.732 AC: 2505 AN: 3422

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.1
DANN	Benign	0.45
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs10768096; hg19: chr11-4591739;