rs6837348

Variant names:

• chr4-111787647-G-A
• rs6837348
• ENST00000751011.1:n.125+14993C>T

Your query was ambiguous. Multiple possible variants found:

• chr4-111787647-G-A
• chr4-111787647-G-T

Variant summary

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

The ENST00000751011.1(ENSG00000297804):​n.125+14993C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.289 in 152,064 control chromosomes in the GnomAD database, including 6,609 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 0.29 (6609 hom., cov: 32)
• Consequence: ENSG00000297804 ENST00000751011.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.47
• Publications: 3 publications found

Genes affected

ENSG00000297804 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.444 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000751011.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297804	ENST00000751011.1		n.125+14993C>T		intron	N/A
	ENSG00000297804	ENST00000751012.1		n.89+14993C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44004 AN: 151946 Hom.: 6602 Cov.: 32

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.238

Gnomad AMR AF: 0.329

Gnomad ASJ AF: 0.239

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.456

Gnomad FIN AF: 0.241

Gnomad MID AF: 0.392

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.276

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

GnomAD4 genome AF: 0.289 AC: 44019 AN: 152064 Hom.: 6609 Cov.: 32 AF XY: 0.292 AC XY: 21724 AN XY: 74330

African (AFR) AF: 0.236 AC: 9795 AN: 41494

American (AMR) AF: 0.329 AC: 5030 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.239 AC: 828 AN: 3470

East Asian (EAS) AF: 0.460 AC: 2372 AN: 5158

South Asian (SAS) AF: 0.456 AC: 2201 AN: 4826

European-Finnish (FIN) AF: 0.241 AC: 2547 AN: 10558

Middle Eastern (MID) AF: 0.398 AC: 117 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20333 AN: 67964

Other (OTH) AF: 0.274 AC: 579 AN: 2114

Alfa AF: 0.294 Hom.: 1060

Bravo AF: 0.290

Asia WGS AF: 0.397 AC: 1377 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.0010
DANN	Benign	0.67
PhyloP100		-4.5

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs6837348;

hg19: chr4-112708803;