rs7907490

Variant names:

• chr10-120163187-T-C
• rs7907490

Your query was ambiguous. Multiple possible variants found:

• chr10-120163187-T-C
• chr10-120163187-T-G

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 0.376 in 152,072 control chromosomes in the GnomAD database, including 11,879 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 0.38 (11879 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.886
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.55 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: 0.376 AC: 57187 AN: 151954 Hom.: 11868 Cov.: 32

Gnomad AFR AF: 0.556

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.297

Gnomad ASJ AF: 0.270

Gnomad EAS AF: 0.190

Gnomad SAS AF: 0.421

Gnomad FIN AF: 0.235

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.336

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

GnomAD4 genome AF: 0.376 AC: 57232 AN: 152072 Hom.: 11879 Cov.: 32 AF XY: 0.371 AC XY: 27568 AN XY: 74342

African (AFR) AF: 0.556 AC: 23043 AN: 41474

American (AMR) AF: 0.296 AC: 4523 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.270 AC: 937 AN: 3470

East Asian (EAS) AF: 0.190 AC: 983 AN: 5172

South Asian (SAS) AF: 0.422 AC: 2037 AN: 4822

European-Finnish (FIN) AF: 0.235 AC: 2479 AN: 10568

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22045 AN: 67978

Other (OTH) AF: 0.333 AC: 703 AN: 2110

Alfa AF: 0.334 Hom.: 14881

Bravo AF: 0.385

Asia WGS AF: 0.313 AC: 1089 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	0.28
DANN	Benign	0.49
PhyloP100		-0.89

Splicing

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

Other links and lift over

dbSNP: rs7907490; hg19: chr10-121922699;