rs7626344

Variant names:

• chr3-180790376-A-G
• rs7626344
• ENST00000485055.5:n.312-8252T>C

Your query was ambiguous. Multiple possible variants found:

• chr3-180790376-A-G
• chr3-180790376-A-T

Variant summary

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

The ENST00000485055.5(ENSG00000285336):​n.312-8252T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.369 in 152,028 control chromosomes in the GnomAD database, including 14,170 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 0.37 (14170 hom., cov: 32)
• Consequence: ENSG00000285336 ENST00000485055.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0700
• Publications: 3 publications found

Genes affected

ENSG00000285336 (HGNC:58949):

ENSG00000145075 (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 (AFR) allele frequency at 95% confidence interval = 0.715 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000485055.5. 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
	LOC101928882	NR_109986.1		n.312-8252T>C		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000285336	ENST00000485055.5	TSL:1	n.312-8252T>C		intron	N/A
	ENSG00000145075	ENST00000471307.6	TSL:3	n.253-8252T>C		intron	N/A
	ENSG00000285336	ENST00000495817.1	TSL:3	n.207-8252T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.369 AC: 55992 AN: 151910 Hom.: 14125 Cov.: 32

Gnomad AFR AF: 0.722

Gnomad AMI AF: 0.163

Gnomad AMR AF: 0.262

Gnomad ASJ AF: 0.331

Gnomad EAS AF: 0.405

Gnomad SAS AF: 0.339

Gnomad FIN AF: 0.182

Gnomad MID AF: 0.301

Gnomad NFE AF: 0.212

Gnomad OTH AF: 0.340

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

GnomAD4 genome AF: 0.369 AC: 56103 AN: 152028 Hom.: 14170 Cov.: 32 AF XY: 0.366 AC XY: 27168 AN XY: 74324

African (AFR) AF: 0.722 AC: 29929 AN: 41454

American (AMR) AF: 0.262 AC: 3999 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.331 AC: 1150 AN: 3470

East Asian (EAS) AF: 0.406 AC: 2100 AN: 5168

South Asian (SAS) AF: 0.339 AC: 1629 AN: 4802

European-Finnish (FIN) AF: 0.182 AC: 1928 AN: 10582

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.212 AC: 14414 AN: 67960

Other (OTH) AF: 0.342 AC: 721 AN: 2110

Alfa AF: 0.262 Hom.: 3477

Bravo AF: 0.390

Asia WGS AF: 0.426 AC: 1479 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	3.9
DANN	Benign	0.53
PhyloP100		0.070

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: rs7626344;

hg19: chr3-180508164;