rs2242661

Variant names:

• chr21-14383500-C-A
• rs2242661
• ENST00000743737.1:n.775C>A

Your query was ambiguous. Multiple possible variants found:

• chr21-14383500-C-A
• chr21-14383500-C-G
• chr21-14383500-C-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000743737.1(ENSG00000296939):​n.775C>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: ENSG00000296939 ENST00000743737.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.40
• Publications: 5 publications found

Genes affected

ENSG00000296939 (HGNC:):

HSPA13 (HGNC:11375): (heat shock protein family A (Hsp70) member 13) The protein encoded by this gene is a member of the heat shock protein 70 family and is found associated with microsomes. Members of this protein family play a role in the processing of cytosolic and secretory proteins, as well as in the removal of denatured or incorrectly-folded proteins. The encoded protein contains an ATPase domain and has been shown to associate with a ubiquitin-like protein. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000743737.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000296939	ENST00000743737.1		n.775C>A		non_coding_transcript_exon	Exon 1 of 2
	ENSG00000296939	ENST00000743739.1		n.81C>A		non_coding_transcript_exon	Exon 1 of 3
	ENSG00000296939	ENST00000743740.1		n.7C>A		non_coding_transcript_exon	Exon 1 of 3

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 78782 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 41356

African (AFR) AF: 0.00 AC: 0 AN: 2522

American (AMR) AF: 0.00 AC: 0 AN: 2178

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2710

East Asian (EAS) AF: 0.00 AC: 0 AN: 3966

South Asian (SAS) AF: 0.00 AC: 0 AN: 8806

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 4348

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 366

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 48840

Other (OTH) AF: 0.00 AC: 0 AN: 5046

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.13
DANN	Benign	0.73
PhyloP100		-2.4
PromoterAI		0.045	Neutral

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs2242661; hg19: chr21-15755821;