rs7912549

Variant names:

• chr10-95069813-G-A
• rs7912549

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 0.822 in 152,002 control chromosomes in the GnomAD database, including 51,793 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 0.82 (51793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.857 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: 0.822 AC: 124887 AN: 151884 Hom.: 51749 Cov.: 32

Gnomad AFR AF: 0.796

Gnomad AMI AF: 0.974

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.844

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.808

Gnomad FIN AF: 0.881

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.863

Gnomad OTH AF: 0.820

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

GnomAD4 genome AF: 0.822 AC: 124980 AN: 152002 Hom.: 51793 Cov.: 32 AF XY: 0.820 AC XY: 60890 AN XY: 74270

African (AFR) AF: 0.796 AC: 33038 AN: 41484

American (AMR) AF: 0.757 AC: 11547 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.844 AC: 2927 AN: 3470

East Asian (EAS) AF: 0.540 AC: 2784 AN: 5160

South Asian (SAS) AF: 0.809 AC: 3901 AN: 4820

European-Finnish (FIN) AF: 0.881 AC: 9263 AN: 10518

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.863 AC: 58662 AN: 67974

Other (OTH) AF: 0.820 AC: 1731 AN: 2110

Alfa AF: 0.814 Hom.: 18368

Bravo AF: 0.807

Asia WGS AF: 0.692 AC: 2391 AN: 3460

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.16
DANN	Benign	0.27
PhyloP100		0.81
PromoterAI		-0.0017	Neutral

Splicing

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

Other links and lift over

dbSNP: rs7912549; hg19: chr10-96829570;