chr7-57639445-C-G

Variant names:

• chr7-57639445-C-G
• rs4870684
• ENST00000511350.2:n.52-2235G>C

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000511350.2(ENSG00000243981):​n.52-2235G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. 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: ENSG00000243981 ENST00000511350.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.217
• Publications: 8 publications found

Genes affected

ENSG00000243981 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000511350.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000243981	ENST00000511350.2	TSL:6	n.52-2235G>C		intron	N/A
	ENSG00000293071	ENST00000605139.1	TSL:5	n.417-2235G>C		intron	N/A
	ENSG00000293071	ENST00000807453.1		n.582-2235G>C		intron	N/A

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

African (AFR) AF: 0.00198 AC: 81 AN: 40934

American (AMR) AF: 0.00341 AC: 52 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.000576 AC: 2 AN: 3472

East Asian (EAS) AF: 0.00 AC: 0 AN: 5128

South Asian (SAS) AF: 0.00829 AC: 40 AN: 4826

European-Finnish (FIN) AF: 0.00104 AC: 11 AN: 10570

Middle Eastern (MID) AF: 0.0103 AC: 3 AN: 292

European-Non Finnish (NFE) AF: 0.00844 AC: 574 AN: 67988

Other (OTH) AF: 0.00524 AC: 11 AN: 2100

Alfa AF: 0.00 Hom.: 16922

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.5
DANN	Benign	0.35
PhyloP100		-0.22
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs4870684; hg19: chr7-57699151;