7-19208655-G-T

Variant names:

• chr7-19208655-G-T
• rs17140875

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.0407 in 152,160 control chromosomes in the GnomAD database, including 169 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 0.041 (169 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.30
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.19).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.116 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: 0.0407 AC: 6192 AN: 152042 Hom.: 171 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.0164

Gnomad AMR AF: 0.0440

Gnomad ASJ AF: 0.0121

Gnomad EAS AF: 0.109

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.0418

Gnomad MID AF: 0.0222

Gnomad NFE AF: 0.0483

Gnomad OTH AF: 0.0454

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

GnomAD4 genome AF: 0.0407 AC: 6192 AN: 152160 Hom.: 169 Cov.: 32 AF XY: 0.0420 AC XY: 3123 AN XY: 74380

African (AFR) AF: 0.0114 AC: 472 AN: 41518

American (AMR) AF: 0.0438 AC: 669 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.0121 AC: 42 AN: 3470

East Asian (EAS) AF: 0.108 AC: 562 AN: 5180

South Asian (SAS) AF: 0.124 AC: 598 AN: 4820

European-Finnish (FIN) AF: 0.0418 AC: 443 AN: 10594

Middle Eastern (MID) AF: 0.0238 AC: 7 AN: 294

European-Non Finnish (NFE) AF: 0.0483 AC: 3285 AN: 67996

Other (OTH) AF: 0.0468 AC: 99 AN: 2116

Alfa AF: 0.0383 Hom.: 130

Bravo AF: 0.0390

Asia WGS AF: 0.122 AC: 426 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.19
CADD	Benign	18
DANN	Benign	0.80
PhyloP100		1.3

Splicing

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

Other links and lift over

dbSNP: rs17140875; hg19: chr7-19248278;