rs4236492

Variant names:

• chr7-149332136-G-A
• rs4236492
• ENST00000820048.1:n.309+1729G>A

Variant summary

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

The ENST00000820048.1(ENSG00000306674):​n.309+1729G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.596 in 151,598 control chromosomes in the GnomAD database, including 29,620 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 0.60 (29620 hom., cov: 32)
• Consequence: ENSG00000306674 ENST00000820048.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.294
• Publications: 2 publications found

Genes affected

ENSG00000306674 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.814 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
ENSG00000306674	ENST00000820048.1	n.309+1729G>A		intron_variant	Intron 1 of 2
ENSG00000306674	ENST00000820049.1	n.402+1729G>A		intron_variant	Intron 1 of 2
ENSG00000306674	ENST00000820050.1	n.374+1754G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.596 AC: 90257 AN: 151480 Hom.: 29609 Cov.: 32

Gnomad AFR AF: 0.294

Gnomad AMI AF: 0.792

Gnomad AMR AF: 0.701

Gnomad ASJ AF: 0.671

Gnomad EAS AF: 0.705

Gnomad SAS AF: 0.834

Gnomad FIN AF: 0.708

Gnomad MID AF: 0.722

Gnomad NFE AF: 0.706

Gnomad OTH AF: 0.618

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

GnomAD4 genome AF: 0.596 AC: 90293 AN: 151598 Hom.: 29620 Cov.: 32 AF XY: 0.601 AC XY: 44489 AN XY: 74042

African (AFR) AF: 0.294 AC: 12173 AN: 41398

American (AMR) AF: 0.701 AC: 10672 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.671 AC: 2325 AN: 3466

East Asian (EAS) AF: 0.705 AC: 3614 AN: 5128

South Asian (SAS) AF: 0.835 AC: 4025 AN: 4820

European-Finnish (FIN) AF: 0.708 AC: 7410 AN: 10462

Middle Eastern (MID) AF: 0.714 AC: 210 AN: 294

European-Non Finnish (NFE) AF: 0.706 AC: 47844 AN: 67802

Other (OTH) AF: 0.618 AC: 1301 AN: 2104

Alfa AF: 0.652 Hom.: 7060

Bravo AF: 0.579

Asia WGS AF: 0.724 AC: 2517 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.2
DANN	Benign	0.58
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs4236492; hg19: chr7-149029227;