7-57639445-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000511350.2(ENSG00000243981):​n.52-2235G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.707 in 151,408 control chromosomes in the GnomAD database, including 38,548 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 0.71 (38548 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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.765 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
ENSG00000243981	ENST00000511350.2	n.52-2235G>A		intron_variant	Intron 1 of 3	6
ENSG00000293071	ENST00000605139.1	n.417-2235G>A		intron_variant	Intron 3 of 4	5
ENSG00000293071	ENST00000807453.1	n.582-2235G>A		intron_variant	Intron 4 of 6

Frequencies

GnomAD3 genomes AF: 0.707 AC: 106937 AN: 151292 Hom.: 38537 Cov.: 30

Gnomad AFR AF: 0.633

Gnomad AMI AF: 0.797

Gnomad AMR AF: 0.707

Gnomad ASJ AF: 0.788

Gnomad EAS AF: 0.466

Gnomad SAS AF: 0.647

Gnomad FIN AF: 0.691

Gnomad MID AF: 0.771

Gnomad NFE AF: 0.770

Gnomad OTH AF: 0.716

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

GnomAD4 genome AF: 0.707 AC: 106987 AN: 151408 Hom.: 38548 Cov.: 30 AF XY: 0.702 AC XY: 51921 AN XY: 73986

African (AFR) AF: 0.633 AC: 25876 AN: 40902

American (AMR) AF: 0.707 AC: 10778 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.788 AC: 2737 AN: 3472

East Asian (EAS) AF: 0.465 AC: 2381 AN: 5124

South Asian (SAS) AF: 0.646 AC: 3117 AN: 4822

European-Finnish (FIN) AF: 0.691 AC: 7302 AN: 10566

Middle Eastern (MID) AF: 0.747 AC: 218 AN: 292

European-Non Finnish (NFE) AF: 0.770 AC: 52349 AN: 67982

Other (OTH) AF: 0.716 AC: 1502 AN: 2098

Alfa AF: 0.735 Hom.: 16922

Bravo AF: 0.708

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.0
DANN	Benign	0.37
PhyloP100		-0.22

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; COSMIC: COSV71413610;