rs6741418

Variant names:

• chr2-190858993-C-T
• rs6741418
• ENST00000772372.1:n.201+9012G>A

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000772372.1(ENSG00000228509):​n.201+9012G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,142 control chromosomes in the GnomAD database, including 1,162 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 0.11 (1162 hom., cov: 32)
• Consequence: ENSG00000228509 ENST00000772372.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.03
• Publications: 5 publications found

Genes affected

ENSG00000228509 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.41).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.154 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000772372.1. 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
	ENSG00000228509	ENST00000772372.1		n.201+9012G>A		intron	N/A
	ENSG00000228509	ENST00000772376.1		n.302+2873G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16274 AN: 152024 Hom.: 1161 Cov.: 32

Gnomad AFR AF: 0.0293

Gnomad AMI AF: 0.259

Gnomad AMR AF: 0.115

Gnomad ASJ AF: 0.186

Gnomad EAS AF: 0.000963

Gnomad SAS AF: 0.0467

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.157

Gnomad OTH AF: 0.130

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

GnomAD4 genome AF: 0.107 AC: 16277 AN: 152142 Hom.: 1162 Cov.: 32 AF XY: 0.105 AC XY: 7772 AN XY: 74368

African (AFR) AF: 0.0293 AC: 1216 AN: 41538

American (AMR) AF: 0.114 AC: 1749 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.186 AC: 645 AN: 3470

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5182

South Asian (SAS) AF: 0.0461 AC: 222 AN: 4818

European-Finnish (FIN) AF: 0.115 AC: 1218 AN: 10566

Middle Eastern (MID) AF: 0.173 AC: 51 AN: 294

European-Non Finnish (NFE) AF: 0.157 AC: 10664 AN: 67974

Other (OTH) AF: 0.129 AC: 272 AN: 2112

Alfa AF: 0.149 Hom.: 2197

Bravo AF: 0.107

Asia WGS AF: 0.0240 AC: 85 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.41
CADD	Benign	17
DANN	Benign	0.75
PhyloP100		3.0

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: rs6741418;

hg19: chr2-191723719;