rs7711912

Variant names:

• chr5-171493699-A-G
• rs7711912
• ENST00000830741.1:n.148+1756T>C

Your query was ambiguous. Multiple possible variants found:

• chr5-171493699-A-G
• chr5-171493699-A-T

Variant summary

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

The ENST00000830741.1(ENSG00000308052):​n.148+1756T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.482 in 151,574 control chromosomes in the GnomAD database, including 18,366 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 0.48 (18366 hom., cov: 30)
• Consequence: ENSG00000308052 ENST00000830741.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.790
• Publications: 6 publications found

Genes affected

ENSG00000308052 (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 (AFR) allele frequency at 95% confidence interval = 0.636 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377721	XR_941213.2	n.132+1756T>C		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000308052	ENST00000830741.1	n.148+1756T>C		intron_variant	Intron 1 of 3
ENSG00000308052	ENST00000830742.1	n.152+1756T>C		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.481 AC: 72902 AN: 151456 Hom.: 18317 Cov.: 30

Gnomad AFR AF: 0.642

Gnomad AMI AF: 0.450

Gnomad AMR AF: 0.456

Gnomad ASJ AF: 0.456

Gnomad EAS AF: 0.284

Gnomad SAS AF: 0.350

Gnomad FIN AF: 0.442

Gnomad MID AF: 0.430

Gnomad NFE AF: 0.422

Gnomad OTH AF: 0.484

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

GnomAD4 genome AF: 0.482 AC: 73009 AN: 151574 Hom.: 18366 Cov.: 30 AF XY: 0.479 AC XY: 35494 AN XY: 74056

African (AFR) AF: 0.643 AC: 26555 AN: 41308

American (AMR) AF: 0.456 AC: 6935 AN: 15196

Ashkenazi Jewish (ASJ) AF: 0.456 AC: 1578 AN: 3464

East Asian (EAS) AF: 0.284 AC: 1461 AN: 5138

South Asian (SAS) AF: 0.351 AC: 1686 AN: 4806

European-Finnish (FIN) AF: 0.442 AC: 4636 AN: 10490

Middle Eastern (MID) AF: 0.429 AC: 126 AN: 294

European-Non Finnish (NFE) AF: 0.422 AC: 28607 AN: 67868

Other (OTH) AF: 0.483 AC: 1017 AN: 2104

Alfa AF: 0.439 Hom.: 63251

Bravo AF: 0.491

Asia WGS AF: 0.368 AC: 1280 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.8
DANN	Benign	0.49
PhyloP100		-0.79

Splicing

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

Other links and lift over

dbSNP: rs7711912; hg19: chr5-170920703;