chr7-45939968-T-G

Variant names:

• chr7-45939968-T-G
• rs2471554

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 0.171 in 152,226 control chromosomes in the GnomAD database, including 2,393 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 0.17 (2393 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 3 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.282 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: 0.171 AC: 25998 AN: 152108 Hom.: 2389 Cov.: 32

Gnomad AFR AF: 0.140

Gnomad AMI AF: 0.152

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.248

Gnomad EAS AF: 0.0330

Gnomad SAS AF: 0.293

Gnomad FIN AF: 0.127

Gnomad MID AF: 0.294

Gnomad NFE AF: 0.194

Gnomad OTH AF: 0.207

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

GnomAD4 genome AF: 0.171 AC: 26024 AN: 152226 Hom.: 2393 Cov.: 32 AF XY: 0.169 AC XY: 12588 AN XY: 74430

African (AFR) AF: 0.140 AC: 5803 AN: 41540

American (AMR) AF: 0.167 AC: 2553 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.248 AC: 862 AN: 3470

East Asian (EAS) AF: 0.0330 AC: 171 AN: 5176

South Asian (SAS) AF: 0.294 AC: 1418 AN: 4818

European-Finnish (FIN) AF: 0.127 AC: 1349 AN: 10610

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.194 AC: 13193 AN: 67996

Other (OTH) AF: 0.213 AC: 451 AN: 2114

Alfa AF: 0.190 Hom.: 962

Bravo AF: 0.169

Asia WGS AF: 0.196 AC: 682 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	4.7
DANN	Benign	0.82
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs2471554; hg19: chr7-45979567;