chr7-57639445-C-G

Position:

• chr7-57639445-C-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The variant allele was found at a frequency of 0.00514 in 151,466 control chromosomes in the GnomAD database, including 8 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 0.0051 (8 hom., cov: 30)
• Consequence: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BS2: High Homozygotes in GnomAd4 at 8 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.57639445C>G		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000243981	ENST00000511350.2	n.52-2235G>C		intron_variant		6
ENSG00000243981	ENST00000605139.1	n.417-2235G>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.00515 AC: 779 AN: 151350 Hom.: 7 Cov.: 30

Gnomad AFR AF: 0.00198

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.00342

Gnomad ASJ AF: 0.000576

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00849

Gnomad FIN AF: 0.00104

Gnomad MID AF: 0.00637

Gnomad NFE AF: 0.00844

Gnomad OTH AF: 0.00577

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

GnomAD4 genome AF: 0.00514 AC: 778 AN: 151466 Hom.: 8 Cov.: 30 AF XY: 0.00489 AC XY: 362 AN XY: 74012

Gnomad4 AFR AF: 0.00198

Gnomad4 AMR AF: 0.00341

Gnomad4 ASJ AF: 0.000576

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00829

Gnomad4 FIN AF: 0.00104

Gnomad4 NFE AF: 0.00844

Gnomad4 OTH AF: 0.00524

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.35

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4870684; hg19: chr7-57699151;