3-164660905-C-G

Variant names:

• chr3-164660905-C-G
• rs2643191
• ENST00000701346.1:n.608-26723C>G

Variant summary

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

The ENST00000701346.1(ENSG00000289884):​n.608-26723C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.527 in 151,888 control chromosomes in the GnomAD database, including 21,880 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 0.53 (21880 hom., cov: 32)
• Consequence: ENSG00000289884 ENST00000701346.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.46
• Publications: 3 publications found

Genes affected

ENSG00000289884 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.684 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000701346.1. 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
	ENSG00000289884	ENST00000701346.1		n.608-26723C>G		intron	N/A
	ENSG00000289884	ENST00000702159.2		n.496-26723C>G		intron	N/A
	ENSG00000289884	ENST00000721983.1		n.278-26723C>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.527 AC: 79923 AN: 151772 Hom.: 21850 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.411

Gnomad AMR AF: 0.478

Gnomad ASJ AF: 0.365

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.521

Gnomad MID AF: 0.440

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.499

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

GnomAD4 genome AF: 0.527 AC: 80001 AN: 151888 Hom.: 21880 Cov.: 32 AF XY: 0.527 AC XY: 39098 AN XY: 74212

African (AFR) AF: 0.691 AC: 28649 AN: 41450

American (AMR) AF: 0.478 AC: 7284 AN: 15226

Ashkenazi Jewish (ASJ) AF: 0.365 AC: 1267 AN: 3472

East Asian (EAS) AF: 0.495 AC: 2542 AN: 5138

South Asian (SAS) AF: 0.495 AC: 2382 AN: 4808

European-Finnish (FIN) AF: 0.521 AC: 5484 AN: 10534

Middle Eastern (MID) AF: 0.456 AC: 134 AN: 294

European-Non Finnish (NFE) AF: 0.454 AC: 30833 AN: 67944

Other (OTH) AF: 0.498 AC: 1052 AN: 2112

Alfa AF: 0.356 Hom.: 952

Bravo AF: 0.532

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.20
DANN	Benign	0.28
PhyloP100		-1.5

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: rs2643191;

hg19: chr3-164378693;