1-60739797-T-C

Variant names:

• chr1-60739797-T-C
• rs1514178
• ENST00000423403.1:n.250-6275A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The ENST00000423403.1(ENSG00000231252):​n.250-6275A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0152 in 152,312 control chromosomes in the GnomAD database, including 21 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 0.015 (21 hom., cov: 33)
• Consequence: ENSG00000231252 ENST00000423403.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.576
• Publications: 8 publications found

Genes affected

ENSG00000231252 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0152 (2316/152312) while in subpopulation NFE AF = 0.0222 (1510/68024). AF 95% confidence interval is 0.0213. There are 21 homozygotes in GnomAd4. There are 1127 alleles in the male GnomAd4 subpopulation. Median coverage is 33. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 21 gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000423403.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LOC101926964	NR_110628.1		n.250-6275A>G		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000231252	ENST00000423403.1	TSL:2	n.250-6275A>G		intron	N/A
	ENSG00000231252	ENST00000634701.1	TSL:5	n.275-6275A>G		intron	N/A
	ENSG00000231252	ENST00000635290.1	TSL:5	n.297-6275A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0152 AC: 2317 AN: 152194 Hom.: 21 Cov.: 33

Gnomad AFR AF: 0.00379

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0217

Gnomad ASJ AF: 0.0150

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000414

Gnomad FIN AF: 0.0216

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0222

Gnomad OTH AF: 0.0143

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

GnomAD4 genome AF: 0.0152 AC: 2316 AN: 152312 Hom.: 21 Cov.: 33 AF XY: 0.0151 AC XY: 1127 AN XY: 74482

African (AFR) AF: 0.00378 AC: 157 AN: 41564

American (AMR) AF: 0.0216 AC: 331 AN: 15302

Ashkenazi Jewish (ASJ) AF: 0.0150 AC: 52 AN: 3470

East Asian (EAS) AF: 0.00 AC: 0 AN: 5184

South Asian (SAS) AF: 0.000414 AC: 2 AN: 4826

European-Finnish (FIN) AF: 0.0216 AC: 229 AN: 10622

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0222 AC: 1510 AN: 68024

Other (OTH) AF: 0.0142 AC: 30 AN: 2114

Alfa AF: 0.0202 Hom.: 121

Bravo AF: 0.0145

Asia WGS AF: 0.00202 AC: 7 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.9
DANN	Benign	0.83
PhyloP100		0.58

Splicing

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

Other links and lift over

dbSNP: rs1514178; hg19: chr1-61205469;