rs438895

Variant names:

• chr1-8278295-G-A
• rs438895
• ENST00000775477.1:n.109-16087G>A

Your query was ambiguous. Multiple possible variants found:

• chr1-8278295-G-A
• chr1-8278295-G-C
• chr1-8278295-G-T

Variant summary

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

The ENST00000775477.1(ENSG00000301006):​n.109-16087G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.847 in 152,094 control chromosomes in the GnomAD database, including 55,827 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 0.85 (55827 hom., cov: 31)
• Consequence: ENSG00000301006 ENST00000775477.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.27
• Publications: 6 publications found

Genes affected

ENSG00000301006 (HGNC:58485):

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 (EAS) allele frequency at 95% confidence interval = 0.963 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000775477.1. 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
	ENSG00000301006	ENST00000775477.1		n.109-16087G>A		intron	N/A
	ENSG00000301006	ENST00000775478.1		n.94-16087G>A		intron	N/A
	ENSG00000301006	ENST00000775479.1		n.89-16087G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.848 AC: 128818 AN: 151976 Hom.: 55826 Cov.: 31

Gnomad AFR AF: 0.654

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.820

Gnomad ASJ AF: 0.948

Gnomad EAS AF: 0.986

Gnomad SAS AF: 0.877

Gnomad FIN AF: 0.969

Gnomad MID AF: 0.908

Gnomad NFE AF: 0.933

Gnomad OTH AF: 0.873

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

GnomAD4 genome AF: 0.847 AC: 128852 AN: 152094 Hom.: 55827 Cov.: 31 AF XY: 0.850 AC XY: 63199 AN XY: 74362

African (AFR) AF: 0.653 AC: 27068 AN: 41448

American (AMR) AF: 0.820 AC: 12524 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.948 AC: 3290 AN: 3472

East Asian (EAS) AF: 0.985 AC: 5087 AN: 5162

South Asian (SAS) AF: 0.878 AC: 4231 AN: 4820

European-Finnish (FIN) AF: 0.969 AC: 10262 AN: 10594

Middle Eastern (MID) AF: 0.915 AC: 269 AN: 294

European-Non Finnish (NFE) AF: 0.933 AC: 63436 AN: 68014

Other (OTH) AF: 0.872 AC: 1839 AN: 2108

Alfa AF: 0.904 Hom.: 252109

Bravo AF: 0.829

Asia WGS AF: 0.901 AC: 3133 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.71
DANN	Benign	0.32
PhyloP100		-1.3

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: rs438895;

hg19: chr1-8338355;

COSMIC: COSV73920364;