rs2040639

Positions:

• chr7-152678103-T-C
• chr7-152678103-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.62 in 151,986 control chromosomes in the GnomAD database, including 30,861 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 0.62 (30861 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.469

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.825 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.620 AC: 94132 AN: 151868 Hom.: 30814 Cov.: 32

Gnomad AFR AF: 0.832

Gnomad AMI AF: 0.346

Gnomad AMR AF: 0.616

Gnomad ASJ AF: 0.590

Gnomad EAS AF: 0.573

Gnomad SAS AF: 0.646

Gnomad FIN AF: 0.386

Gnomad MID AF: 0.614

Gnomad NFE AF: 0.535

Gnomad OTH AF: 0.609

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

GnomAD4 genome AF: 0.620 AC: 94238 AN: 151986 Hom.: 30861 Cov.: 32 AF XY: 0.614 AC XY: 45590 AN XY: 74276

Gnomad4 AFR AF: 0.833

Gnomad4 AMR AF: 0.616

Gnomad4 ASJ AF: 0.590

Gnomad4 EAS AF: 0.573

Gnomad4 SAS AF: 0.645

Gnomad4 FIN AF: 0.386

Gnomad4 NFE AF: 0.535

Gnomad4 OTH AF: 0.611

Alfa AF: 0.545 Hom.: 31769

Bravo AF: 0.644

Asia WGS AF: 0.629 AC: 2185 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	4.4
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2040639; hg19: chr7-152375188;