rs2395174

Variant names:

• chr6-32437101-T-G
• rs2395174
• ENST00000766007.1:n.279+1043A>C

Variant summary

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

The ENST00000766007.1(ENSG00000299747):​n.279+1043A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.238 in 152,122 control chromosomes in the GnomAD database, including 4,871 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 (4871 hom., cov: 31)
• Consequence: ENSG00000299747 ENST00000766007.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.400
• Publications: 34 publications found

Genes affected

ENSG00000299747 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.75).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.285 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000766007.1. 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
	ENSG00000299747	ENST00000766007.1		n.279+1043A>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.238 AC: 36219 AN: 152004 Hom.: 4869 Cov.: 31

Gnomad AFR AF: 0.145

Gnomad AMI AF: 0.326

Gnomad AMR AF: 0.212

Gnomad ASJ AF: 0.150

Gnomad EAS AF: 0.160

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.413

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.289

Gnomad OTH AF: 0.236

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

GnomAD4 genome AF: 0.238 AC: 36242 AN: 152122 Hom.: 4871 Cov.: 31 AF XY: 0.241 AC XY: 17896 AN XY: 74348

African (AFR) AF: 0.145 AC: 6023 AN: 41534

American (AMR) AF: 0.211 AC: 3227 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.150 AC: 519 AN: 3468

East Asian (EAS) AF: 0.160 AC: 828 AN: 5178

South Asian (SAS) AF: 0.175 AC: 846 AN: 4824

European-Finnish (FIN) AF: 0.413 AC: 4355 AN: 10550

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.289 AC: 19622 AN: 67970

Other (OTH) AF: 0.234 AC: 493 AN: 2108

Alfa AF: 0.253 Hom.: 3965

Bravo AF: 0.220

Asia WGS AF: 0.203 AC: 710 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.75
CADD	Benign	0.30
DANN	Benign	0.86
PhyloP100		-0.40

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: rs2395174;

hg19: chr6-32404878;