rs1251078

chr1-75723803-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000648424.1(ENSG00000293044):n.108+139G>C variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.628 in 152,072 control chromosomes in the GnomAD database, including 30,090 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 0.63 (30088 hom., cov: 33)
  • Exomes 𝑓: 0.75 (2 hom.)
• Consequence: ENST00000648424.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.703 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SLC44A5	XM_017000610.2	c.-247+139G>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000648424.1	n.108+139G>C		intron_variant, non_coding_transcript_variant
	ENST00000433521.2	n.71-15G>C		splice_polypyrimidine_tract_variant, intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.628 AC: 95374 AN: 151944 Hom.: 30070 Cov.: 33

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.637

Gnomad AMR AF: 0.532

Gnomad ASJ AF: 0.722

Gnomad EAS AF: 0.713

Gnomad SAS AF: 0.724

Gnomad FIN AF: 0.614

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.599

Gnomad OTH AF: 0.628

GnomAD4 exome AF: 0.750 AC: 6 AN: 8 Hom.: 2 Cov.: 0 AF XY: 0.500 AC XY: 2 AN XY: 4

Gnomad4 FIN exome AF: 0.833

Gnomad4 NFE exome AF: 0.500

GnomAD4 genome AF: 0.628 AC: 95439 AN: 152064 Hom.: 30088 Cov.: 33 AF XY: 0.629 AC XY: 46745 AN XY: 74308

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.531

Gnomad4 ASJ AF: 0.722

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.723

Gnomad4 FIN AF: 0.614

Gnomad4 NFE AF: 0.599

Gnomad4 OTH AF: 0.629

Alfa AF: 0.609 Hom.: 3508

Bravo AF: 0.621

Asia WGS AF: 0.686 AC: 2385 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.27
Dann	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1251078; hg19: chr1-76189488;