2-163819403-T-C

Variant names:

• chr2-163819403-T-C
• rs16848941
• ENST00000429636.1:n.379+49746A>G

Variant summary

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

The ENST00000429636.1(ENSG00000237844):​n.379+49746A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.121 in 152,138 control chromosomes in the GnomAD database, including 1,261 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 0.12 (1261 hom., cov: 32)
• Consequence: ENSG00000237844 ENST00000429636.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521
• Publications: 2 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.141 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.379+49746A>G		intron	N/A
	ENSG00000237844	ENST00000666867.1		n.454+48296A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.121 AC: 18375 AN: 152020 Hom.: 1258 Cov.: 32

Gnomad AFR AF: 0.0896

Gnomad AMI AF: 0.291

Gnomad AMR AF: 0.111

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0464

Gnomad SAS AF: 0.139

Gnomad FIN AF: 0.119

Gnomad MID AF: 0.117

Gnomad NFE AF: 0.143

Gnomad OTH AF: 0.139

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

GnomAD4 genome AF: 0.121 AC: 18389 AN: 152138 Hom.: 1261 Cov.: 32 AF XY: 0.120 AC XY: 8913 AN XY: 74392

African (AFR) AF: 0.0894 AC: 3714 AN: 41522

American (AMR) AF: 0.111 AC: 1687 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.142 AC: 492 AN: 3470

East Asian (EAS) AF: 0.0465 AC: 241 AN: 5180

South Asian (SAS) AF: 0.141 AC: 678 AN: 4824

European-Finnish (FIN) AF: 0.119 AC: 1265 AN: 10594

Middle Eastern (MID) AF: 0.112 AC: 33 AN: 294

European-Non Finnish (NFE) AF: 0.143 AC: 9714 AN: 67968

Other (OTH) AF: 0.142 AC: 301 AN: 2114

Alfa AF: 0.0942 Hom.: 163

Bravo AF: 0.118

Asia WGS AF: 0.118 AC: 409 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.77
PhyloP100		0.52
Mutation Taster		=100/0	polymorphism

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: rs16848941;

hg19: chr2-164675913;