10-103367521-A-G

Variant names:

• chr10-103367521-A-G
• rs11191666

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 0.406 in 151,516 control chromosomes in the GnomAD database, including 13,281 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 0.41 (13281 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.358
• Publications: 16 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.74).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.623 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: 0.406 AC: 61516 AN: 151396 Hom.: 13278 Cov.: 29

Gnomad AFR AF: 0.262

Gnomad AMI AF: 0.382

Gnomad AMR AF: 0.435

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.643

Gnomad FIN AF: 0.485

Gnomad MID AF: 0.529

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.409

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

GnomAD4 genome AF: 0.406 AC: 61544 AN: 151516 Hom.: 13281 Cov.: 29 AF XY: 0.411 AC XY: 30457 AN XY: 74018

African (AFR) AF: 0.262 AC: 10829 AN: 41340

American (AMR) AF: 0.435 AC: 6610 AN: 15206

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1593 AN: 3460

East Asian (EAS) AF: 0.434 AC: 2226 AN: 5126

South Asian (SAS) AF: 0.642 AC: 3091 AN: 4814

European-Finnish (FIN) AF: 0.485 AC: 5063 AN: 10442

Middle Eastern (MID) AF: 0.531 AC: 154 AN: 290

European-Non Finnish (NFE) AF: 0.454 AC: 30771 AN: 67822

Other (OTH) AF: 0.408 AC: 859 AN: 2104

Alfa AF: 0.435 Hom.: 31415

Bravo AF: 0.391

Asia WGS AF: 0.514 AC: 1784 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.74
CADD	Benign	4.2
DANN	Benign	0.29
PhyloP100		0.36
PromoterAI		0.080	Neutral

Splicing

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

Other links and lift over

dbSNP: rs11191666; hg19: chr10-105127278;