rs7912549

Variant names:

• chr10-95069813-G-A
• rs7912549

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP6 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. Variant has been reported in Lovd as Likely benign (no stars).

• Frequency: Genomes: 𝑓 0.82 (51793 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.814

ACMG classification

Verdict is Benign. Variant got -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BP6: Variant 10-95069813-G-A is Benign according to our data. Variant chr10-95069813-G-A is described in Lovd as [Likely_benign].
• 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

Gnomad4 AFR AF: 0.796

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.844

Gnomad4 EAS AF: 0.540

Gnomad4 SAS AF: 0.809

Gnomad4 FIN AF: 0.881

Gnomad4 NFE AF: 0.863

Gnomad4 OTH AF: 0.820

Alfa AF: 0.818 Hom.: 8785

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7912549; hg19: chr10-96829570;