chr15-91596949-G-A

Variant names:

• chr15-91596949-G-A
• rs4632107
• ENST00000555947.7:n.231-7928G>A

Variant summary

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

The ENST00000555947.7(CRAT37):​n.231-7928G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.523 in 151,948 control chromosomes in the GnomAD database, including 23,131 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 0.52 (23131 hom., cov: 31)
• Consequence: CRAT37 ENST00000555947.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.04
• Publications: 4 publications found

Genes affected

CRAT37 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.666 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000555947.7. 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
	CRAT37	ENST00000555947.7	TSL:4	n.231-7928G>A		intron	N/A
	CRAT37	ENST00000664984.1		n.353-7928G>A		intron	N/A
	CRAT37	ENST00000687281.2		n.349+12229G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.523 AC: 79444 AN: 151830 Hom.: 23130 Cov.: 31

Gnomad AFR AF: 0.299

Gnomad AMI AF: 0.714

Gnomad AMR AF: 0.452

Gnomad ASJ AF: 0.612

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.633

Gnomad MID AF: 0.605

Gnomad NFE AF: 0.672

Gnomad OTH AF: 0.556

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

GnomAD4 genome AF: 0.523 AC: 79454 AN: 151948 Hom.: 23131 Cov.: 31 AF XY: 0.518 AC XY: 38477 AN XY: 74272

African (AFR) AF: 0.298 AC: 12350 AN: 41426

American (AMR) AF: 0.451 AC: 6887 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.612 AC: 2124 AN: 3470

East Asian (EAS) AF: 0.255 AC: 1321 AN: 5172

South Asian (SAS) AF: 0.513 AC: 2474 AN: 4818

European-Finnish (FIN) AF: 0.633 AC: 6686 AN: 10556

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.672 AC: 45618 AN: 67934

Other (OTH) AF: 0.555 AC: 1168 AN: 2106

Alfa AF: 0.616 Hom.: 95799

Bravo AF: 0.495

Asia WGS AF: 0.376 AC: 1311 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	5.1
DANN	Benign	0.72
PhyloP100		1.0

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: rs4632107;

hg19: chr15-92140179;