chr7-71008019-C-T

Variant names:

• chr7-71008019-C-T
• rs1525293

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 0.33 in 151,984 control chromosomes in the GnomAD database, including 8,860 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 0.33 (8860 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0110
• Publications: 5 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.449 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: 0.331 AC: 50207 AN: 151866 Hom.: 8862 Cov.: 33

Gnomad AFR AF: 0.191

Gnomad AMI AF: 0.349

Gnomad AMR AF: 0.390

Gnomad ASJ AF: 0.435

Gnomad EAS AF: 0.464

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.472

Gnomad NFE AF: 0.376

Gnomad OTH AF: 0.385

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

GnomAD4 genome AF: 0.330 AC: 50206 AN: 151984 Hom.: 8860 Cov.: 33 AF XY: 0.334 AC XY: 24803 AN XY: 74278

African (AFR) AF: 0.191 AC: 7918 AN: 41466

American (AMR) AF: 0.389 AC: 5953 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.435 AC: 1507 AN: 3468

East Asian (EAS) AF: 0.465 AC: 2396 AN: 5156

South Asian (SAS) AF: 0.318 AC: 1532 AN: 4818

European-Finnish (FIN) AF: 0.391 AC: 4118 AN: 10530

Middle Eastern (MID) AF: 0.459 AC: 135 AN: 294

European-Non Finnish (NFE) AF: 0.376 AC: 25528 AN: 67946

Other (OTH) AF: 0.379 AC: 802 AN: 2114

Alfa AF: 0.360 Hom.: 7166

Bravo AF: 0.330

Asia WGS AF: 0.344 AC: 1198 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	3.0
DANN	Benign	0.63
PhyloP100		0.011

Splicing

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

Other links and lift over

dbSNP: rs1525293; hg19: chr7-70473005;