rs10485949

Positions:

• chr7-49258329-G-A
• chr7-49258329-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.0929 in 151,958 control chromosomes in the GnomAD database, including 741 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 0.093 (741 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.31

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.0928 AC: 14098 AN: 151842 Hom.: 739 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.0471

Gnomad ASJ AF: 0.0282

Gnomad EAS AF: 0.167

Gnomad SAS AF: 0.0980

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.0253

Gnomad NFE AF: 0.0757

Gnomad OTH AF: 0.0798

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

GnomAD4 genome AF: 0.0929 AC: 14120 AN: 151958 Hom.: 741 Cov.: 33 AF XY: 0.0954 AC XY: 7088 AN XY: 74274

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.0469

Gnomad4 ASJ AF: 0.0282

Gnomad4 EAS AF: 0.167

Gnomad4 SAS AF: 0.0989

Gnomad4 FIN AF: 0.145

Gnomad4 NFE AF: 0.0757

Gnomad4 OTH AF: 0.0813

Alfa AF: 0.0429 Hom.: 40

Bravo AF: 0.0866

Asia WGS AF: 0.114 AC: 397 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.050
DANN	Benign	0.49

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10485949; hg19: chr7-49297925;