rs2642265

Variant names:

• chr7-24213443-C-A
• rs2642265
• ENST00000745616.1:n.217C>A

Your query was ambiguous. Multiple possible variants found:

• chr7-24213443-C-A
• chr7-24213443-C-T

Variant summary

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

The ENST00000745616.1(ENSG00000297122):​n.217C>A 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 0.327 in 152,058 control chromosomes in the GnomAD database, including 8,814 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 0.33 (8814 hom., cov: 32)
• Consequence: ENSG00000297122 ENST00000745616.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.07
• Publications: 2 publications found

Genes affected

ENSG00000297122 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.552 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000745616.1. 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
	ENSG00000297122	ENST00000745616.1		n.217C>A		non_coding_transcript_exon	Exon 2 of 4
	ENSG00000228944	ENST00000439839.1	TSL:5	n.160-16414G>T		intron	N/A
	ENSG00000228944	ENST00000718234.1		n.320-16414G>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.327 AC: 49619 AN: 151940 Hom.: 8800 Cov.: 32

Gnomad AFR AF: 0.429

Gnomad AMI AF: 0.225

Gnomad AMR AF: 0.360

Gnomad ASJ AF: 0.246

Gnomad EAS AF: 0.570

Gnomad SAS AF: 0.419

Gnomad FIN AF: 0.318

Gnomad MID AF: 0.231

Gnomad NFE AF: 0.239

Gnomad OTH AF: 0.324

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

GnomAD4 genome AF: 0.327 AC: 49677 AN: 152058 Hom.: 8814 Cov.: 32 AF XY: 0.334 AC XY: 24865 AN XY: 74342

African (AFR) AF: 0.429 AC: 17802 AN: 41462

American (AMR) AF: 0.360 AC: 5510 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.246 AC: 853 AN: 3468

East Asian (EAS) AF: 0.570 AC: 2936 AN: 5154

South Asian (SAS) AF: 0.420 AC: 2029 AN: 4828

European-Finnish (FIN) AF: 0.318 AC: 3363 AN: 10568

Middle Eastern (MID) AF: 0.235 AC: 69 AN: 294

European-Non Finnish (NFE) AF: 0.239 AC: 16223 AN: 67968

Other (OTH) AF: 0.326 AC: 687 AN: 2108

Alfa AF: 0.303 Hom.: 1334

Bravo AF: 0.334

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	5.9
DANN	Benign	0.76
PhyloP100		1.1

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: rs2642265;

hg19: chr7-24253062;