chr17-19590865-C-A

Variant names:

• chr17-19590865-C-A
• rs2245639

Variant summary

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

The variant allele was found at a frequency of 0.555 in 152,026 control chromosomes in the GnomAD database, including 24,191 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 0.56 (24191 hom., cov: 32)
  • Exomes 𝑓: 0.17 (0 hom.)
• Consequence: SLC47A1P1 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.140
• Publications: 8 publications found

Genes affected

SLC47A1P1 (HGNC:51849): (SLC47A1 pseudogene 1)

ENSG00000290454 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.931 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC47A1P1		n.19590865C>A		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000290454	ENST00000420951.1	n.273-3345C>A		intron_variant	Intron 2 of 4	5
SLC47A1P1	ENST00000449666.3	n.652+77C>A		intron_variant	Intron 5 of 7	6
ENSG00000262769	ENST00000574267.1	n.26+7032G>T		intron_variant	Intron 1 of 3	5

Frequencies

GnomAD3 genomes AF: 0.555 AC: 84342 AN: 151900 Hom.: 24149 Cov.: 32

Gnomad AFR AF: 0.488

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.666

Gnomad ASJ AF: 0.482

Gnomad EAS AF: 0.953

Gnomad SAS AF: 0.681

Gnomad FIN AF: 0.489

Gnomad MID AF: 0.535

Gnomad NFE AF: 0.545

Gnomad OTH AF: 0.555

GnomAD4 exome AF: 0.167 AC: 1 AN: 6 Hom.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.555 AC: 84435 AN: 152020 Hom.: 24191 Cov.: 32 AF XY: 0.562 AC XY: 41735 AN XY: 74306

African (AFR) AF: 0.488 AC: 20230 AN: 41414

American (AMR) AF: 0.666 AC: 10184 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.482 AC: 1675 AN: 3472

East Asian (EAS) AF: 0.953 AC: 4936 AN: 5180

South Asian (SAS) AF: 0.681 AC: 3282 AN: 4818

European-Finnish (FIN) AF: 0.489 AC: 5169 AN: 10562

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.545 AC: 37070 AN: 67970

Other (OTH) AF: 0.560 AC: 1182 AN: 2112

Alfa AF: 0.542 Hom.: 30156

Bravo AF: 0.563

Asia WGS AF: 0.805 AC: 2796 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.6
DANN	Benign	0.61
PhyloP100		0.14

Splicing

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

Other links and lift over

dbSNP: rs2245639; hg19: chr17-19494178;