rs1343444

Variant names:

• chr6-48587331-C-G
• rs1343444
• ENST00000730502.1:n.283-9854C>G

Variant summary

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

The ENST00000730502.1(ENSG00000295504):​n.283-9854C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.152 in 151,738 control chromosomes in the GnomAD database, including 2,700 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 0.15 (2700 hom., cov: 32)
• Consequence: ENSG00000295504 ENST00000730502.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.06
• Publications: 0 publications found

Genes affected

ENSG00000295504 (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 (EAS) allele frequency at 95% confidence interval = 0.487 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000730502.1. 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
	ENSG00000295504	ENST00000730502.1		n.283-9854C>G		intron	N/A
	ENSG00000295504	ENST00000730503.1		n.127-9854C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.152 AC: 22990 AN: 151620 Hom.: 2679 Cov.: 32

Gnomad AFR AF: 0.195

Gnomad AMI AF: 0.00548

Gnomad AMR AF: 0.299

Gnomad ASJ AF: 0.0991

Gnomad EAS AF: 0.503

Gnomad SAS AF: 0.206

Gnomad FIN AF: 0.0699

Gnomad MID AF: 0.0759

Gnomad NFE AF: 0.0792

Gnomad OTH AF: 0.151

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

GnomAD4 genome AF: 0.152 AC: 23036 AN: 151738 Hom.: 2700 Cov.: 32 AF XY: 0.155 AC XY: 11518 AN XY: 74178

African (AFR) AF: 0.195 AC: 8089 AN: 41438

American (AMR) AF: 0.300 AC: 4559 AN: 15182

Ashkenazi Jewish (ASJ) AF: 0.0991 AC: 343 AN: 3462

East Asian (EAS) AF: 0.503 AC: 2591 AN: 5152

South Asian (SAS) AF: 0.205 AC: 989 AN: 4818

European-Finnish (FIN) AF: 0.0699 AC: 741 AN: 10604

Middle Eastern (MID) AF: 0.0850 AC: 25 AN: 294

European-Non Finnish (NFE) AF: 0.0791 AC: 5363 AN: 67766

Other (OTH) AF: 0.157 AC: 331 AN: 2110

Alfa AF: 0.122 Hom.: 226

Bravo AF: 0.177

Asia WGS AF: 0.340 AC: 1179 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	3.5
DANN	Benign	0.68
PhyloP100		1.1

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: rs1343444;

hg19: chr6-48555067;