rs1932397

Variant names:

• chr1-29590350-C-T
• rs1932397
• ENST00000772656.1:n.173+5688C>T

Variant summary

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

The ENST00000772656.1(ENSG00000300547):​n.173+5688C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.142 in 152,186 control chromosomes in the GnomAD database, including 1,899 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 0.14 (1899 hom., cov: 32)
• Consequence: ENSG00000300547 ENST00000772656.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.305
• Publications: 3 publications found

Genes affected

ENSG00000300547 (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 (EAS) allele frequency at 95% confidence interval = 0.335 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000300547	ENST00000772656.1	n.173+5688C>T		intron_variant	Intron 2 of 4
ENSG00000300547	ENST00000772657.1	n.187+5688C>T		intron_variant	Intron 2 of 3
ENSG00000300547	ENST00000772658.1	n.170+5688C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.142 AC: 21579 AN: 152068 Hom.: 1899 Cov.: 32

Gnomad AFR AF: 0.0499

Gnomad AMI AF: 0.0702

Gnomad AMR AF: 0.167

Gnomad ASJ AF: 0.184

Gnomad EAS AF: 0.349

Gnomad SAS AF: 0.124

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.170

Gnomad OTH AF: 0.153

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

GnomAD4 genome AF: 0.142 AC: 21580 AN: 152186 Hom.: 1899 Cov.: 32 AF XY: 0.143 AC XY: 10624 AN XY: 74410

African (AFR) AF: 0.0499 AC: 2072 AN: 41546

American (AMR) AF: 0.168 AC: 2563 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.184 AC: 640 AN: 3470

East Asian (EAS) AF: 0.349 AC: 1800 AN: 5164

South Asian (SAS) AF: 0.123 AC: 592 AN: 4820

European-Finnish (FIN) AF: 0.177 AC: 1879 AN: 10600

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.170 AC: 11586 AN: 67980

Other (OTH) AF: 0.157 AC: 331 AN: 2110

Alfa AF: 0.164 Hom.: 3551

Bravo AF: 0.141

Asia WGS AF: 0.217 AC: 755 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	3.8
DANN	Benign	0.59
PhyloP100		0.30

Splicing

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

Other links and lift over

dbSNP: rs1932397; hg19: chr1-30063197;