rs4897081

Variant names:

• chr6-149115402-G-A
• rs4897081
• ENST00000834740.1:n.229-40848C>T

Your query was ambiguous. Multiple possible variants found:

• chr6-149115402-G-A
• chr6-149115402-G-T

Variant summary

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

The ENST00000834740.1(ENSG00000308521):​n.229-40848C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.414 in 151,954 control chromosomes in the GnomAD database, including 13,464 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 0.41 (13464 hom., cov: 31)
• Consequence: ENSG00000308521 ENST00000834740.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.109
• Publications: 5 publications found

Genes affected

ENSG00000308521 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.517 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000834740.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308521	ENST00000834740.1		n.229-40848C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.413 AC: 62755 AN: 151836 Hom.: 13437 Cov.: 31

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.269

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.491

Gnomad EAS AF: 0.283

Gnomad SAS AF: 0.391

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.363

Gnomad OTH AF: 0.441

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

GnomAD4 genome AF: 0.414 AC: 62844 AN: 151954 Hom.: 13464 Cov.: 31 AF XY: 0.415 AC XY: 30809 AN XY: 74272

African (AFR) AF: 0.523 AC: 21648 AN: 41416

American (AMR) AF: 0.394 AC: 6027 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.491 AC: 1705 AN: 3470

East Asian (EAS) AF: 0.283 AC: 1460 AN: 5156

South Asian (SAS) AF: 0.391 AC: 1882 AN: 4818

European-Finnish (FIN) AF: 0.394 AC: 4149 AN: 10534

Middle Eastern (MID) AF: 0.391 AC: 115 AN: 294

European-Non Finnish (NFE) AF: 0.363 AC: 24681 AN: 67964

Other (OTH) AF: 0.441 AC: 932 AN: 2112

Alfa AF: 0.384 Hom.: 43753

Bravo AF: 0.420

Asia WGS AF: 0.406 AC: 1408 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	3.1
DANN	Benign	0.65
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs4897081; hg19: chr6-149436538;