rs7644410

Variant names:

• chr3-30499934-A-G
• rs7644410
• ENST00000813769.1:n.180-12665T>C

Variant summary

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

The ENST00000813769.1(ENSG00000227549):​n.180-12665T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.313 in 151,952 control chromosomes in the GnomAD database, including 7,744 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 0.31 (7744 hom., cov: 32)
• Consequence: ENSG00000227549 ENST00000813769.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00
• Publications: 1 publications found

Genes affected

ENSG00000227549 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.401 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000813769.1. 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
	ENSG00000227549	ENST00000813769.1		n.180-12665T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.313 AC: 47589 AN: 151834 Hom.: 7741 Cov.: 32

Gnomad AFR AF: 0.243

Gnomad AMI AF: 0.290

Gnomad AMR AF: 0.316

Gnomad ASJ AF: 0.351

Gnomad EAS AF: 0.417

Gnomad SAS AF: 0.265

Gnomad FIN AF: 0.353

Gnomad MID AF: 0.241

Gnomad NFE AF: 0.344

Gnomad OTH AF: 0.323

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

GnomAD4 genome AF: 0.313 AC: 47618 AN: 151952 Hom.: 7744 Cov.: 32 AF XY: 0.313 AC XY: 23257 AN XY: 74274

African (AFR) AF: 0.243 AC: 10057 AN: 41420

American (AMR) AF: 0.316 AC: 4829 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.351 AC: 1218 AN: 3470

East Asian (EAS) AF: 0.416 AC: 2142 AN: 5152

South Asian (SAS) AF: 0.265 AC: 1275 AN: 4818

European-Finnish (FIN) AF: 0.353 AC: 3725 AN: 10546

Middle Eastern (MID) AF: 0.241 AC: 71 AN: 294

European-Non Finnish (NFE) AF: 0.344 AC: 23345 AN: 67952

Other (OTH) AF: 0.328 AC: 692 AN: 2112

Alfa AF: 0.304 Hom.: 1075

Bravo AF: 0.312

Asia WGS AF: 0.346 AC: 1202 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.67
PhyloP100		0.0

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: rs7644410;

hg19: chr3-30541426;