rs11938704

Variant names:

• chr4-144522218-A-C
• rs11938704
• ENST00000649263.1:n.328-106240T>G

Your query was ambiguous. Multiple possible variants found:

• chr4-144522218-A-C
• chr4-144522218-A-G

Variant summary

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

The ENST00000649263.1(ENSG00000285713):​n.328-106240T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,070 control chromosomes in the GnomAD database, including 5,408 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 0.24 (5408 hom., cov: 32)
• Consequence: ENSG00000285713 ENST00000649263.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.283
• Publications: 6 publications found

Genes affected

ENSG00000285713 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.398 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000649263.1. 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
	ENSG00000285713	ENST00000649263.1		n.328-106240T>G		intron	N/A	ENSP00000497507.1	A0A3B3ISY7
	ENSG00000285783	ENST00000650526.1		n.223-106240T>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35729 AN: 151952 Hom.: 5396 Cov.: 32

Gnomad AFR AF: 0.403

Gnomad AMI AF: 0.101

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.174

Gnomad EAS AF: 0.311

Gnomad SAS AF: 0.320

Gnomad FIN AF: 0.0780

Gnomad MID AF: 0.188

Gnomad NFE AF: 0.139

Gnomad OTH AF: 0.223

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

GnomAD4 genome AF: 0.235 AC: 35772 AN: 152070 Hom.: 5408 Cov.: 32 AF XY: 0.235 AC XY: 17452 AN XY: 74332

African (AFR) AF: 0.403 AC: 16708 AN: 41458

American (AMR) AF: 0.288 AC: 4405 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.174 AC: 603 AN: 3472

East Asian (EAS) AF: 0.312 AC: 1605 AN: 5150

South Asian (SAS) AF: 0.319 AC: 1536 AN: 4818

European-Finnish (FIN) AF: 0.0780 AC: 828 AN: 10610

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.139 AC: 9466 AN: 67978

Other (OTH) AF: 0.226 AC: 477 AN: 2110

Alfa AF: 0.189 Hom.: 1425

Bravo AF: 0.256

Asia WGS AF: 0.383 AC: 1325 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.66
DANN	Benign	0.45
PhyloP100		-0.28

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: rs11938704;

hg19: chr4-145443370;