chr7-37905144-G-A

Variant names:

• chr7-37905144-G-A
• rs4720265
• ENST00000476620.1:c.-37-43696G>A

Variant summary

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

The ENST00000476620.1(ENSG00000290149):​c.-37-43696G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.233 in 152,034 control chromosomes in the GnomAD database, including 4,165 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 0.23 (4165 hom., cov: 32)
• Consequence: ENSG00000290149 ENST00000476620.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0320
• Publications: 8 publications found

Genes affected

ENSG00000290149 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.238 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000476620.1. 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
	ENSG00000290149	ENST00000476620.1	TSL:4	c.-37-43696G>A		intron	N/A	ENSP00000425858.1	D6RIH7

Frequencies

GnomAD3 genomes AF: 0.233 AC: 35427 AN: 151916 Hom.: 4160 Cov.: 32

Gnomad AFR AF: 0.216

Gnomad AMI AF: 0.211

Gnomad AMR AF: 0.234

Gnomad ASJ AF: 0.273

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.233

Gnomad FIN AF: 0.245

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.241

Gnomad OTH AF: 0.228

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

GnomAD4 genome AF: 0.233 AC: 35456 AN: 152034 Hom.: 4165 Cov.: 32 AF XY: 0.233 AC XY: 17319 AN XY: 74304

African (AFR) AF: 0.216 AC: 8949 AN: 41468

American (AMR) AF: 0.234 AC: 3571 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.273 AC: 949 AN: 3470

East Asian (EAS) AF: 0.221 AC: 1143 AN: 5164

South Asian (SAS) AF: 0.233 AC: 1124 AN: 4822

European-Finnish (FIN) AF: 0.245 AC: 2592 AN: 10562

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.241 AC: 16391 AN: 67954

Other (OTH) AF: 0.227 AC: 479 AN: 2108

Alfa AF: 0.243 Hom.: 5897

Bravo AF: 0.235

Asia WGS AF: 0.230 AC: 800 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.6
DANN	Benign	0.81
PhyloP100		-0.032
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

Other links and lift over

dbSNP: rs4720265; hg19: chr7-37944746;