rs1418968

Variant names:

• chr6-18772867-G-A
• rs1418968
• ENST00000840172.1:n.73-5231C>T

Variant summary

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

The ENST00000840172.1(ENSG00000309302):​n.73-5231C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.171 in 152,030 control chromosomes in the GnomAD database, including 3,371 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 0.17 (3371 hom., cov: 32)
• Consequence: ENSG00000309302 ENST00000840172.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.347
• Publications: 0 publications found

Genes affected

ENSG00000309302 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.354 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000840172.1. 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
	ENSG00000309302	ENST00000840172.1		n.73-5231C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.171 AC: 25934 AN: 151912 Hom.: 3368 Cov.: 32

Gnomad AFR AF: 0.359

Gnomad AMI AF: 0.0921

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0813

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.145

Gnomad FIN AF: 0.0913

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.0793

Gnomad OTH AF: 0.166

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

GnomAD4 genome AF: 0.171 AC: 25972 AN: 152030 Hom.: 3371 Cov.: 32 AF XY: 0.170 AC XY: 12656 AN XY: 74348

African (AFR) AF: 0.359 AC: 14851 AN: 41404

American (AMR) AF: 0.176 AC: 2680 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.0813 AC: 282 AN: 3470

East Asian (EAS) AF: 0.123 AC: 637 AN: 5162

South Asian (SAS) AF: 0.144 AC: 696 AN: 4818

European-Finnish (FIN) AF: 0.0913 AC: 967 AN: 10596

Middle Eastern (MID) AF: 0.120 AC: 35 AN: 292

European-Non Finnish (NFE) AF: 0.0792 AC: 5389 AN: 68006

Other (OTH) AF: 0.167 AC: 351 AN: 2104

Alfa AF: 0.107 Hom.: 2071

Bravo AF: 0.185

Asia WGS AF: 0.148 AC: 514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.44
PhyloP100		0.35

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: rs1418968;

hg19: chr6-18773098;