rs7691507

Variant names:

• chr4-55076834-T-C
• rs7691507
• ENST00000511222.1:n.233+1592T>C

Variant summary

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

The ENST00000511222.1(ENSG00000250646):​n.233+1592T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.278 in 151,944 control chromosomes in the GnomAD database, including 7,457 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 0.28 (7457 hom., cov: 31)
• Consequence: ENSG00000250646 ENST00000511222.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00200
• Publications: 12 publications found

Genes affected

ENSG00000250646 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.497 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
ENSG00000250646	ENST00000511222.1	n.233+1592T>C		intron_variant	Intron 3 of 3	5

Frequencies

GnomAD3 genomes AF: 0.278 AC: 42150 AN: 151826 Hom.: 7428 Cov.: 31

Gnomad AFR AF: 0.502

Gnomad AMI AF: 0.120

Gnomad AMR AF: 0.160

Gnomad ASJ AF: 0.352

Gnomad EAS AF: 0.154

Gnomad SAS AF: 0.203

Gnomad FIN AF: 0.189

Gnomad MID AF: 0.344

Gnomad NFE AF: 0.195

Gnomad OTH AF: 0.265

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

GnomAD4 genome AF: 0.278 AC: 42221 AN: 151944 Hom.: 7457 Cov.: 31 AF XY: 0.274 AC XY: 20380 AN XY: 74268

African (AFR) AF: 0.502 AC: 20793 AN: 41398

American (AMR) AF: 0.160 AC: 2441 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.352 AC: 1222 AN: 3472

East Asian (EAS) AF: 0.153 AC: 790 AN: 5148

South Asian (SAS) AF: 0.203 AC: 976 AN: 4808

European-Finnish (FIN) AF: 0.189 AC: 1999 AN: 10592

Middle Eastern (MID) AF: 0.336 AC: 98 AN: 292

European-Non Finnish (NFE) AF: 0.195 AC: 13236 AN: 67948

Other (OTH) AF: 0.264 AC: 557 AN: 2110

Alfa AF: 0.240 Hom.: 10183

Bravo AF: 0.284

Asia WGS AF: 0.221 AC: 769 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.6
DANN	Benign	0.51
PhyloP100		-0.0020

Splicing

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

Other links and lift over

dbSNP: rs7691507; hg19: chr4-55943001;