1-232311645-C-T

Variant names:

• chr1-232311645-C-T
• rs1631842
• ENST00000808822.1:n.374+1077G>A

Variant summary

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

The ENST00000808822.1(ENSG00000305110):​n.374+1077G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.372 in 152,066 control chromosomes in the GnomAD database, including 11,309 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 0.37 (11309 hom., cov: 32)
• Consequence: ENSG00000305110 ENST00000808822.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.924
• Publications: 2 publications found

Genes affected

ENSG00000305110 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.448 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000808822.1. 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
	ENSG00000305110	ENST00000808822.1		n.374+1077G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.373 AC: 56606 AN: 151946 Hom.: 11312 Cov.: 32

Gnomad AFR AF: 0.250

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.216

Gnomad SAS AF: 0.457

Gnomad FIN AF: 0.346

Gnomad MID AF: 0.497

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.398

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

GnomAD4 genome AF: 0.372 AC: 56632 AN: 152066 Hom.: 11309 Cov.: 32 AF XY: 0.368 AC XY: 27370 AN XY: 74338

African (AFR) AF: 0.250 AC: 10381 AN: 41512

American (AMR) AF: 0.365 AC: 5580 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1587 AN: 3470

East Asian (EAS) AF: 0.216 AC: 1117 AN: 5160

South Asian (SAS) AF: 0.456 AC: 2199 AN: 4818

European-Finnish (FIN) AF: 0.346 AC: 3650 AN: 10550

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30707 AN: 67958

Other (OTH) AF: 0.401 AC: 845 AN: 2108

Alfa AF: 0.427 Hom.: 58801

Bravo AF: 0.366

Asia WGS AF: 0.323 AC: 1130 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.66
DANN	Benign	0.65
PhyloP100		-0.92

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: rs1631842;

hg19: chr1-232447391;