rs11938795

Variant names:

• chr4-122151854-T-C
• rs11938795
• ENST00000827168.1:n.374A>G

Variant summary

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

The ENST00000827168.1(ENSG00000307570):​n.374A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,188 control chromosomes in the GnomAD database, including 4,773 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 (4773 hom., cov: 33)
• Consequence: ENSG00000307570 ENST00000827168.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.103
• Publications: 19 publications found

Genes affected

ENSG00000307570 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.308 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000827168.1. 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
	ENSG00000307570	ENST00000827168.1		n.374A>G		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36517 AN: 152070 Hom.: 4774 Cov.: 33

Gnomad AFR AF: 0.313

Gnomad AMI AF: 0.338

Gnomad AMR AF: 0.183

Gnomad ASJ AF: 0.249

Gnomad EAS AF: 0.0457

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.129

Gnomad MID AF: 0.209

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.252

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

GnomAD4 genome AF: 0.240 AC: 36533 AN: 152188 Hom.: 4773 Cov.: 33 AF XY: 0.230 AC XY: 17122 AN XY: 74430

African (AFR) AF: 0.313 AC: 12984 AN: 41508

American (AMR) AF: 0.183 AC: 2794 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.249 AC: 865 AN: 3468

East Asian (EAS) AF: 0.0452 AC: 235 AN: 5194

South Asian (SAS) AF: 0.124 AC: 601 AN: 4828

European-Finnish (FIN) AF: 0.129 AC: 1367 AN: 10596

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.247 AC: 16793 AN: 67984

Other (OTH) AF: 0.248 AC: 525 AN: 2114

Alfa AF: 0.245 Hom.: 7713

Bravo AF: 0.249

Asia WGS AF: 0.120 AC: 419 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	6.1
DANN	Benign	0.55
PhyloP100		0.10
PromoterAI		0.011	Neutral

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: rs11938795;

hg19: chr4-123073009;