rs7912549

Positions:

• chr10-95069813-G-A

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/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	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;