7-38070471-A-T

Variant names:

• chr7-38070471-A-T
• rs6974574

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 0.646 in 152,000 control chromosomes in the GnomAD database, including 31,888 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 0.65 (31888 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00700
• Publications: 14 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.656 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes AF: 0.645 AC: 98021 AN: 151882 Hom.: 31849 Cov.: 31

Gnomad AFR AF: 0.639

Gnomad AMI AF: 0.652

Gnomad AMR AF: 0.533

Gnomad ASJ AF: 0.676

Gnomad EAS AF: 0.675

Gnomad SAS AF: 0.628

Gnomad FIN AF: 0.750

Gnomad MID AF: 0.687

Gnomad NFE AF: 0.655

Gnomad OTH AF: 0.647

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

GnomAD4 genome AF: 0.646 AC: 98125 AN: 152000 Hom.: 31888 Cov.: 31 AF XY: 0.647 AC XY: 48079 AN XY: 74286

African (AFR) AF: 0.639 AC: 26490 AN: 41432

American (AMR) AF: 0.533 AC: 8140 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.676 AC: 2343 AN: 3466

East Asian (EAS) AF: 0.675 AC: 3488 AN: 5166

South Asian (SAS) AF: 0.629 AC: 3031 AN: 4816

European-Finnish (FIN) AF: 0.750 AC: 7925 AN: 10564

Middle Eastern (MID) AF: 0.701 AC: 206 AN: 294

European-Non Finnish (NFE) AF: 0.655 AC: 44541 AN: 67974

Other (OTH) AF: 0.650 AC: 1368 AN: 2106

Alfa AF: 0.641 Hom.: 3911

Bravo AF: 0.632

Asia WGS AF: 0.636 AC: 2210 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.9
DANN	Benign	0.49
PhyloP100		-0.0070

Splicing

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

Other links and lift over

dbSNP: rs6974574; hg19: chr7-38110073;