rs6721348

Positions:

• chr2-172253781-G-A
• chr2-172253781-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000662340.1(ENSG00000232555):​n.213-44416G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.877 in 151,972 control chromosomes in the GnomAD database, including 58,636 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 0.88 (58636 hom., cov: 28)
• Consequence: ENSG00000232555 ENST00000662340.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.359

Genes affected

ENSG00000232555 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.904 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC107985960	XR_001739773.3	n.2208+1148G>A		intron_variant
LOC107985960	XR_001739775.3	n.2208+1148G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000232555	ENST00000662340.1	n.213-44416G>A		intron_variant
ENSG00000232555	ENST00000667725.1	n.242-44416G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.877 AC: 133185 AN: 151854 Hom.: 58613 Cov.: 28

Gnomad AFR AF: 0.802

Gnomad AMI AF: 0.933

Gnomad AMR AF: 0.900

Gnomad ASJ AF: 0.916

Gnomad EAS AF: 0.881

Gnomad SAS AF: 0.845

Gnomad FIN AF: 0.920

Gnomad MID AF: 0.902

Gnomad NFE AF: 0.910

Gnomad OTH AF: 0.883

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

GnomAD4 genome AF: 0.877 AC: 133255 AN: 151972 Hom.: 58636 Cov.: 28 AF XY: 0.879 AC XY: 65339 AN XY: 74298

Gnomad4 AFR AF: 0.802

Gnomad4 AMR AF: 0.900

Gnomad4 ASJ AF: 0.916

Gnomad4 EAS AF: 0.882

Gnomad4 SAS AF: 0.846

Gnomad4 FIN AF: 0.920

Gnomad4 NFE AF: 0.910

Gnomad4 OTH AF: 0.878

Alfa AF: 0.900 Hom.: 79879

Bravo AF: 0.873

Asia WGS AF: 0.826 AC: 2874 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	2.6
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6721348; hg19: chr2-173118509;