chr7-38065431-T-G

Variant names:

• chr7-38065431-T-G
• rs1717725

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 0.247 in 151,898 control chromosomes in the GnomAD database, including 4,708 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 0.25 (4708 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.247 AC: 37466 AN: 151780 Hom.: 4706 Cov.: 32

Gnomad AFR AF: 0.241

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.202

Gnomad ASJ AF: 0.286

Gnomad EAS AF: 0.202

Gnomad SAS AF: 0.376

Gnomad FIN AF: 0.209

Gnomad MID AF: 0.364

Gnomad NFE AF: 0.257

Gnomad OTH AF: 0.249

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

GnomAD4 genome AF: 0.247 AC: 37485 AN: 151898 Hom.: 4708 Cov.: 32 AF XY: 0.248 AC XY: 18407 AN XY: 74240

African (AFR) AF: 0.241 AC: 9964 AN: 41396

American (AMR) AF: 0.202 AC: 3086 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.286 AC: 993 AN: 3468

East Asian (EAS) AF: 0.202 AC: 1039 AN: 5144

South Asian (SAS) AF: 0.378 AC: 1818 AN: 4814

European-Finnish (FIN) AF: 0.209 AC: 2207 AN: 10536

Middle Eastern (MID) AF: 0.361 AC: 106 AN: 294

European-Non Finnish (NFE) AF: 0.257 AC: 17463 AN: 67946

Other (OTH) AF: 0.248 AC: 522 AN: 2104

Alfa AF: 0.260 Hom.: 1982

Bravo AF: 0.246

Asia WGS AF: 0.245 AC: 852 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	7.3
DANN	Benign	0.38
PhyloP100		0.87

Splicing

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

Other links and lift over

dbSNP: rs1717725; hg19: chr7-38105033;