chr7-109512654-A-G

Variant names:

• chr7-109512654-A-G
• rs10953615

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 0.289 in 151,950 control chromosomes in the GnomAD database, including 6,743 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 0.29 (6743 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.566
• Publications: 13 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.331 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: 0.289 AC: 43847 AN: 151832 Hom.: 6742 Cov.: 31

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.425

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.224

Gnomad FIN AF: 0.344

Gnomad MID AF: 0.361

Gnomad NFE AF: 0.335

Gnomad OTH AF: 0.294

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

GnomAD4 genome AF: 0.289 AC: 43873 AN: 151950 Hom.: 6743 Cov.: 31 AF XY: 0.287 AC XY: 21345 AN XY: 74250

African (AFR) AF: 0.206 AC: 8560 AN: 41492

American (AMR) AF: 0.325 AC: 4947 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1270 AN: 3470

East Asian (EAS) AF: 0.106 AC: 546 AN: 5160

South Asian (SAS) AF: 0.224 AC: 1081 AN: 4820

European-Finnish (FIN) AF: 0.344 AC: 3629 AN: 10544

Middle Eastern (MID) AF: 0.367 AC: 108 AN: 294

European-Non Finnish (NFE) AF: 0.335 AC: 22724 AN: 67930

Other (OTH) AF: 0.295 AC: 621 AN: 2104

Alfa AF: 0.317 Hom.: 18725

Bravo AF: 0.284

Asia WGS AF: 0.192 AC: 667 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	8.0
DANN	Benign	0.68
PhyloP100		0.57

Splicing

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

Other links and lift over

dbSNP: rs10953615; hg19: chr7-109152711;