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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC105377462	XR_939272.3	n.165-22698T>G		intron_variant	Intron 1 of 7
LOC105377462	XR_939273.3	n.164+39766T>G		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285713	ENST00000649263.1	n.328-106240T>G		intron_variant	Intron 4 of 8			ENSP00000497507.1
ENSG00000285783	ENST00000650526.1	n.223-106240T>G		intron_variant	Intron 2 of 14

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 v4.3

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

Other links and lift over

dbSNP: rs11938704; hg19: chr4-145443370;