2-191534731-G-C

Variant names:

• chr2-191534731-G-C
• rs1949429
• ENST00000810035.1:n.260+11818G>C

Variant summary

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

The ENST00000810035.1(ENSG00000305283):​n.260+11818G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,910 control chromosomes in the GnomAD database, including 12,771 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 0.40 (12771 hom., cov: 32)
• Consequence: ENSG00000305283 ENST00000810035.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.855
• Publications: 4 publications found

Genes affected

ENSG00000305283 (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 (NFE) allele frequency at 95% confidence interval = 0.461 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985833	XR_001739229.1	n.161+11818G>C		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000305283	ENST00000810035.1	n.260+11818G>C		intron_variant	Intron 3 of 6
ENSG00000305283	ENST00000810036.1	n.206+21820G>C		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60448 AN: 151792 Hom.: 12768 Cov.: 32

Gnomad AFR AF: 0.266

Gnomad AMI AF: 0.407

Gnomad AMR AF: 0.406

Gnomad ASJ AF: 0.494

Gnomad EAS AF: 0.255

Gnomad SAS AF: 0.407

Gnomad FIN AF: 0.504

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.465

Gnomad OTH AF: 0.407

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

GnomAD4 genome AF: 0.398 AC: 60452 AN: 151910 Hom.: 12771 Cov.: 32 AF XY: 0.399 AC XY: 29628 AN XY: 74242

African (AFR) AF: 0.265 AC: 10991 AN: 41436

American (AMR) AF: 0.406 AC: 6203 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.494 AC: 1713 AN: 3466

East Asian (EAS) AF: 0.253 AC: 1305 AN: 5148

South Asian (SAS) AF: 0.407 AC: 1957 AN: 4814

European-Finnish (FIN) AF: 0.504 AC: 5292 AN: 10508

Middle Eastern (MID) AF: 0.445 AC: 130 AN: 292

European-Non Finnish (NFE) AF: 0.466 AC: 31638 AN: 67958

Other (OTH) AF: 0.404 AC: 853 AN: 2112

Alfa AF: 0.432 Hom.: 1815

Bravo AF: 0.380

Asia WGS AF: 0.321 AC: 1119 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.68
PhyloP100		-0.85

Splicing

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

Other links and lift over

dbSNP: rs1949429; hg19: chr2-192399457;