chr2-164106976-T-C

Variant names:

• chr2-164106976-T-C
• rs1446468
• ENST00000429636.1:n.196+143744A>G

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.196+143744A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.406 in 151,988 control chromosomes in the GnomAD database, including 15,346 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 0.41 (15346 hom., cov: 31)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0630
• Publications: 34 publications found

Genes affected

ENSG00000237844 (HGNC:58942):

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 (NFE) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000429636.1. 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
	ENSG00000237844	ENST00000429636.1	TSL:3	n.196+143744A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.407 AC: 61779 AN: 151870 Hom.: 15351 Cov.: 31

Gnomad AFR AF: 0.120

Gnomad AMI AF: 0.390

Gnomad AMR AF: 0.392

Gnomad ASJ AF: 0.454

Gnomad EAS AF: 0.537

Gnomad SAS AF: 0.415

Gnomad FIN AF: 0.622

Gnomad MID AF: 0.272

Gnomad NFE AF: 0.540

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.406 AC: 61772 AN: 151988 Hom.: 15346 Cov.: 31 AF XY: 0.412 AC XY: 30585 AN XY: 74280

African (AFR) AF: 0.119 AC: 4951 AN: 41476

American (AMR) AF: 0.392 AC: 5980 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.454 AC: 1575 AN: 3472

East Asian (EAS) AF: 0.537 AC: 2769 AN: 5154

South Asian (SAS) AF: 0.413 AC: 1991 AN: 4816

European-Finnish (FIN) AF: 0.622 AC: 6564 AN: 10560

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.540 AC: 36669 AN: 67926

Other (OTH) AF: 0.399 AC: 841 AN: 2110

Alfa AF: 0.414 Hom.: 10505

Bravo AF: 0.374

Asia WGS AF: 0.480 AC: 1669 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	2.0
DANN	Benign	0.67
PhyloP100		-0.063

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs1446468; hg19: chr2-164963486;