7-100704471-A-T

Variant names:

• chr7-100704471-A-T
• rs221770

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 0.893 in 152,080 control chromosomes in the GnomAD database, including 60,693 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 0.89 (60693 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 = 0.921 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: 0.893 AC: 135682 AN: 151962 Hom.: 60652 Cov.: 31

Gnomad AFR AF: 0.886

Gnomad AMI AF: 0.842

Gnomad AMR AF: 0.934

Gnomad ASJ AF: 0.967

Gnomad EAS AF: 0.936

Gnomad SAS AF: 0.866

Gnomad FIN AF: 0.832

Gnomad MID AF: 0.981

Gnomad NFE AF: 0.891

Gnomad OTH AF: 0.918

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

GnomAD4 genome AF: 0.893 AC: 135778 AN: 152080 Hom.: 60693 Cov.: 31 AF XY: 0.892 AC XY: 66266 AN XY: 74302

African (AFR) AF: 0.886 AC: 36764 AN: 41494

American (AMR) AF: 0.934 AC: 14256 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.967 AC: 3359 AN: 3472

East Asian (EAS) AF: 0.936 AC: 4850 AN: 5182

South Asian (SAS) AF: 0.867 AC: 4180 AN: 4824

European-Finnish (FIN) AF: 0.832 AC: 8757 AN: 10524

Middle Eastern (MID) AF: 0.980 AC: 288 AN: 294

European-Non Finnish (NFE) AF: 0.891 AC: 60616 AN: 68008

Other (OTH) AF: 0.919 AC: 1940 AN: 2112

Alfa AF: 0.883 Hom.: 6928

Bravo AF: 0.902

Asia WGS AF: 0.891 AC: 3100 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.82
DANN	Benign	0.47
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs221770; hg19: chr7-100302094;