rs13237474

Variant names:

• chr7-135816721-C-T
• rs13237474
• ENST00000419211.3:n.607+41606C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000419211.3(ENSG00000224746):​n.607+41606C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0228 in 152,202 control chromosomes in the GnomAD database, including 56 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 0.023 (56 hom., cov: 32)
• Consequence: ENSG00000224746 ENST00000419211.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.668
• Publications: 3 publications found

Genes affected

ENSG00000224746 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0228 (3465/152202) while in subpopulation NFE AF = 0.0334 (2270/68016). AF 95% confidence interval is 0.0322. There are 56 homozygotes in GnomAd4. There are 1703 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 56 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000224746	ENST00000419211.3	n.607+41606C>T		intron_variant	Intron 1 of 2	2
ENSG00000224746	ENST00000830862.1	n.609+41606C>T		intron_variant	Intron 1 of 2
ENSG00000224746	ENST00000830863.1	n.615+41606C>T		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0228 AC: 3464 AN: 152084 Hom.: 56 Cov.: 32

Gnomad AFR AF: 0.00640

Gnomad AMI AF: 0.0450

Gnomad AMR AF: 0.0151

Gnomad ASJ AF: 0.0164

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00435

Gnomad FIN AF: 0.0498

Gnomad MID AF: 0.00955

Gnomad NFE AF: 0.0334

Gnomad OTH AF: 0.0239

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

GnomAD4 genome AF: 0.0228 AC: 3465 AN: 152202 Hom.: 56 Cov.: 32 AF XY: 0.0229 AC XY: 1703 AN XY: 74404

African (AFR) AF: 0.00638 AC: 265 AN: 41526

American (AMR) AF: 0.0150 AC: 230 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0164 AC: 57 AN: 3466

East Asian (EAS) AF: 0.000193 AC: 1 AN: 5180

South Asian (SAS) AF: 0.00435 AC: 21 AN: 4824

European-Finnish (FIN) AF: 0.0498 AC: 527 AN: 10582

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0334 AC: 2270 AN: 68016

Other (OTH) AF: 0.0237 AC: 50 AN: 2114

Alfa AF: 0.0258 Hom.: 10

Bravo AF: 0.0198

Asia WGS AF: 0.00144 AC: 5 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.2
DANN	Benign	0.48
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs13237474; hg19: chr7-135501469;