7-107719560-C-T

Variant names:

• chr7-107719560-C-T
• rs2028030

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 0.435 in 151,954 control chromosomes in the GnomAD database, including 14,537 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 0.44 (14537 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 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: 0.435 AC: 66112 AN: 151836 Hom.: 14549 Cov.: 31

Gnomad AFR AF: 0.390

Gnomad AMI AF: 0.502

Gnomad AMR AF: 0.440

Gnomad ASJ AF: 0.477

Gnomad EAS AF: 0.629

Gnomad SAS AF: 0.390

Gnomad FIN AF: 0.463

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.443

Gnomad OTH AF: 0.438

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

GnomAD4 genome AF: 0.435 AC: 66121 AN: 151954 Hom.: 14537 Cov.: 31 AF XY: 0.437 AC XY: 32417 AN XY: 74252

African (AFR) AF: 0.390 AC: 16154 AN: 41442

American (AMR) AF: 0.440 AC: 6720 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.477 AC: 1653 AN: 3468

East Asian (EAS) AF: 0.628 AC: 3237 AN: 5154

South Asian (SAS) AF: 0.390 AC: 1877 AN: 4808

European-Finnish (FIN) AF: 0.463 AC: 4880 AN: 10544

Middle Eastern (MID) AF: 0.350 AC: 103 AN: 294

European-Non Finnish (NFE) AF: 0.443 AC: 30117 AN: 67950

Other (OTH) AF: 0.437 AC: 922 AN: 2112

Alfa AF: 0.436 Hom.: 7993

Bravo AF: 0.436

Asia WGS AF: 0.486 AC: 1695 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.70
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs2028030; hg19: chr7-107360005; COSMIC: COSV55917114;