rs10499559

Variant names:

• chr7-22069841-G-A
• rs10499559

Your query was ambiguous. Multiple possible variants found:

• chr7-22069841-G-A
• chr7-22069841-G-C
• chr7-22069841-G-T

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 0.121 in 152,116 control chromosomes in the GnomAD database, including 1,418 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 0.12 (1418 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.356
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 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: 0.121 AC: 18390 AN: 151998 Hom.: 1416 Cov.: 32

Gnomad AFR AF: 0.0704

Gnomad AMI AF: 0.141

Gnomad AMR AF: 0.0776

Gnomad ASJ AF: 0.0597

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.0910

Gnomad FIN AF: 0.226

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.134

Gnomad OTH AF: 0.108

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

GnomAD4 genome AF: 0.121 AC: 18393 AN: 152116 Hom.: 1418 Cov.: 32 AF XY: 0.126 AC XY: 9396 AN XY: 74356

African (AFR) AF: 0.0703 AC: 2917 AN: 41504

American (AMR) AF: 0.0774 AC: 1183 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.0597 AC: 207 AN: 3466

East Asian (EAS) AF: 0.344 AC: 1773 AN: 5150

South Asian (SAS) AF: 0.0906 AC: 437 AN: 4822

European-Finnish (FIN) AF: 0.226 AC: 2389 AN: 10568

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.134 AC: 9090 AN: 67994

Other (OTH) AF: 0.111 AC: 235 AN: 2116

Alfa AF: 0.131 Hom.: 6593

Bravo AF: 0.112

Asia WGS AF: 0.174 AC: 607 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.90
DANN	Benign	0.23
PhyloP100		-0.36

Splicing

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

Other links and lift over

dbSNP: rs10499559; hg19: chr7-22109459;