chr2-57760458-T-C

Variant names:

• chr2-57760458-T-C
• rs11682175
• ENST00000605503.2:n.361-4254T>C

Variant summary

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

The ENST00000605503.2(ENSG00000293318):​n.361-4254T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.385 in 152,094 control chromosomes in the GnomAD database, including 12,224 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 0.39 (12224 hom., cov: 32)
• Consequence: ENSG00000293318 ENST00000605503.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.499
• Publications: 53 publications found

Genes affected

ENSG00000293318 (HGNC:):

ENSG00000285755 (HGNC:58935):

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 (NFE) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000605503.2. 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
	ENSG00000293318	ENST00000605503.2	TSL:4	n.361-4254T>C		intron	N/A
	ENSG00000293611	ENST00000715879.1		n.499-13737A>G		intron	N/A
	ENSG00000293611	ENST00000715880.1		n.162-13737A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.385 AC: 58586 AN: 151976 Hom.: 12224 Cov.: 32

Gnomad AFR AF: 0.218

Gnomad AMI AF: 0.555

Gnomad AMR AF: 0.396

Gnomad ASJ AF: 0.524

Gnomad EAS AF: 0.385

Gnomad SAS AF: 0.396

Gnomad FIN AF: 0.391

Gnomad MID AF: 0.465

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.420

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

GnomAD4 genome AF: 0.385 AC: 58596 AN: 152094 Hom.: 12224 Cov.: 32 AF XY: 0.381 AC XY: 28331 AN XY: 74348

African (AFR) AF: 0.217 AC: 9017 AN: 41500

American (AMR) AF: 0.396 AC: 6046 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.524 AC: 1817 AN: 3470

East Asian (EAS) AF: 0.386 AC: 1998 AN: 5178

South Asian (SAS) AF: 0.397 AC: 1913 AN: 4816

European-Finnish (FIN) AF: 0.391 AC: 4140 AN: 10576

Middle Eastern (MID) AF: 0.466 AC: 137 AN: 294

European-Non Finnish (NFE) AF: 0.473 AC: 32147 AN: 67970

Other (OTH) AF: 0.414 AC: 876 AN: 2114

Alfa AF: 0.444 Hom.: 32690

Bravo AF: 0.379

Asia WGS AF: 0.362 AC: 1260 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	4.9
DANN	Benign	0.46
PhyloP100		0.50

Splicing

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

Other links and lift over

dbSNP: rs11682175; hg19: chr2-57987593;