1-97057448-G-A

Variant names:

• chr1-97057448-G-A
• rs12132152
• ENST00000737657.1:n.549+9843G>A

Variant summary

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

The ENST00000737657.1(ENSG00000296260):​n.549+9843G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0223 in 152,168 control chromosomes in the GnomAD database, including 46 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 0.022 (46 hom., cov: 32)
• Consequence: ENSG00000296260 ENST00000737657.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.335

Genes affected

ENSG00000296260 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BS1: Variant frequency is greater than expected in population nfe. GnomAd4 allele frequency = 0.0223 (3392/152168) while in subpopulation NFE AF = 0.0327 (2223/68004). AF 95% confidence interval is 0.0316. There are 46 homozygotes in GnomAd4. There are 1581 alleles in the male GnomAd4 subpopulation. Median coverage is 32. This position passed quality control check.
• BS2: High Homozygotes in GnomAd4 at 46 gene

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
ENSG00000296260	ENST00000737657.1	n.549+9843G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.0223 AC: 3395 AN: 152050 Hom.: 46 Cov.: 32

Gnomad AFR AF: 0.0101

Gnomad AMI AF: 0.0219

Gnomad AMR AF: 0.0219

Gnomad ASJ AF: 0.0167

Gnomad EAS AF: 0.000193

Gnomad SAS AF: 0.00519

Gnomad FIN AF: 0.0229

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0327

Gnomad OTH AF: 0.0287

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

GnomAD4 genome AF: 0.0223 AC: 3392 AN: 152168 Hom.: 46 Cov.: 32 AF XY: 0.0213 AC XY: 1581 AN XY: 74382

African (AFR) AF: 0.0100 AC: 416 AN: 41512

American (AMR) AF: 0.0219 AC: 334 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0167 AC: 58 AN: 3470

East Asian (EAS) AF: 0.000194 AC: 1 AN: 5160

South Asian (SAS) AF: 0.00540 AC: 26 AN: 4816

European-Finnish (FIN) AF: 0.0229 AC: 243 AN: 10602

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0327 AC: 2223 AN: 68004

Other (OTH) AF: 0.0284 AC: 60 AN: 2112

Alfa AF: 0.0307 Hom.: 161

Bravo AF: 0.0221

Asia WGS AF: 0.00577 AC: 20 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	5.5
DANN	Benign	0.67
PhyloP100		0.34

Splicing

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

Publications

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Other links and lift over

dbSNP: rs12132152; hg19: chr1-97523004;