7-107839870-T-C

Variant names:

• chr7-107839870-T-C
• rs4380874

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 0.674 in 152,174 control chromosomes in the GnomAD database, including 35,339 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 0.67 (35339 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.33
• Publications: 37 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.849 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: 0.674 AC: 102483 AN: 152056 Hom.: 35291 Cov.: 32

Gnomad AFR AF: 0.805

Gnomad AMI AF: 0.674

Gnomad AMR AF: 0.658

Gnomad ASJ AF: 0.626

Gnomad EAS AF: 0.872

Gnomad SAS AF: 0.579

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.640

Gnomad NFE AF: 0.600

Gnomad OTH AF: 0.667

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

GnomAD4 genome AF: 0.674 AC: 102586 AN: 152174 Hom.: 35339 Cov.: 32 AF XY: 0.676 AC XY: 50277 AN XY: 74384

African (AFR) AF: 0.806 AC: 33458 AN: 41522

American (AMR) AF: 0.659 AC: 10066 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.626 AC: 2172 AN: 3468

East Asian (EAS) AF: 0.871 AC: 4510 AN: 5180

South Asian (SAS) AF: 0.579 AC: 2789 AN: 4818

European-Finnish (FIN) AF: 0.625 AC: 6611 AN: 10584

Middle Eastern (MID) AF: 0.637 AC: 186 AN: 292

European-Non Finnish (NFE) AF: 0.600 AC: 40775 AN: 68004

Other (OTH) AF: 0.666 AC: 1406 AN: 2112

Alfa AF: 0.621 Hom.: 55089

Bravo AF: 0.684

Asia WGS AF: 0.748 AC: 2603 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.1
DANN	Benign	0.64
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs4380874; hg19: chr7-107480315;