2-163819403-T-C

Position:

• chr2-163819403-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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: intergenic_region
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.521

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
		n.163819403T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000237844	ENST00000429636.1	n.379+49746A>G		intron_variant		3
ENSG00000237844	ENST00000666867.1	n.454+48296A>G		intron_variant

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

Gnomad4 AFR AF: 0.0894

Gnomad4 AMR AF: 0.111

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0465

Gnomad4 SAS AF: 0.141

Gnomad4 FIN AF: 0.119

Gnomad4 NFE AF: 0.143

Gnomad4 OTH AF: 0.142

Alfa AF: 0.0941 Hom.: 162

Bravo AF: 0.118

Asia WGS AF: 0.118 AC: 409 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	5.0
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs16848941; hg19: chr2-164675913;