rs7711337

Variant names:

• chr5-162656512-G-A
• rs7711337
• ENST00000644348.1:n.26-32298C>T

Your query was ambiguous. Multiple possible variants found:

• chr5-162656512-G-A
• chr5-162656512-G-C

Variant summary

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

The ENST00000644348.1(ENSG00000254186):​n.26-32298C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.425 in 151,856 control chromosomes in the GnomAD database, including 14,765 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 0.43 (14765 hom., cov: 31)
• Consequence: ENSG00000254186 ENST00000644348.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.646
• Publications: 9 publications found

Genes affected

ENSG00000254186 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.544 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000644348.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000254186	ENST00000644348.1		n.26-32298C>T		intron	N/A
	ENSG00000254186	ENST00000646617.1		n.1148+3590C>T		intron	N/A
	ENSG00000254186	ENST00000660514.1		n.713+3590C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.425 AC: 64542 AN: 151738 Hom.: 14743 Cov.: 31

Gnomad AFR AF: 0.549

Gnomad AMI AF: 0.518

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.427

Gnomad EAS AF: 0.0371

Gnomad SAS AF: 0.243

Gnomad FIN AF: 0.292

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.420

Gnomad OTH AF: 0.436

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

GnomAD4 genome AF: 0.425 AC: 64609 AN: 151856 Hom.: 14765 Cov.: 31 AF XY: 0.411 AC XY: 30538 AN XY: 74212

African (AFR) AF: 0.550 AC: 22740 AN: 41376

American (AMR) AF: 0.386 AC: 5880 AN: 15238

Ashkenazi Jewish (ASJ) AF: 0.427 AC: 1482 AN: 3470

East Asian (EAS) AF: 0.0372 AC: 192 AN: 5168

South Asian (SAS) AF: 0.243 AC: 1169 AN: 4810

European-Finnish (FIN) AF: 0.292 AC: 3077 AN: 10546

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.420 AC: 28552 AN: 67938

Other (OTH) AF: 0.434 AC: 916 AN: 2112

Alfa AF: 0.427 Hom.: 30891

Bravo AF: 0.442

Asia WGS AF: 0.189 AC: 662 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.45
DANN	Benign	0.50
PhyloP100		-0.65

Splicing

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

Other links and lift over

dbSNP: rs7711337; hg19: chr5-162083518;