rs1251078

Variant names:

• chr1-75723803-C-G
• rs1251078
• XM_017000610.2:c.-247+139G>C

Variant summary

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

The ENST00000746415.1(ENSG00000297240):​n.598C>G variant causes a non coding transcript exon 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: ENSG00000297240 ENST00000746415.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.451
• Publications: 8 publications found

Genes affected

SLC44A5 (HGNC:28524): (solute carrier family 44 member 5) Predicted to enable transmembrane transporter activity. Predicted to be involved in transmembrane transport. Predicted to be located in plasma membrane. Predicted to be active in membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000297240 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000746415.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000297240	ENST00000746415.1		n.598C>G		non_coding_transcript_exon	Exon 1 of 1
	ENSG00000293044	ENST00000433521.2	TSL:3	n.71-15G>C		intron	N/A
	ENSG00000293044	ENST00000648424.1		n.108+139G>C		intron	N/A

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

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: 0.833 AC: 5 AN: 6

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 1 AN: 2

Other (OTH) AC: 0 AN: 0

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

African (AFR) AF: 0.684 AC: 28358 AN: 41482

American (AMR) AF: 0.531 AC: 8116 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.722 AC: 2503 AN: 3468

East Asian (EAS) AF: 0.713 AC: 3688 AN: 5174

South Asian (SAS) AF: 0.723 AC: 3488 AN: 4826

European-Finnish (FIN) AF: 0.614 AC: 6478 AN: 10544

Middle Eastern (MID) AF: 0.654 AC: 191 AN: 292

European-Non Finnish (NFE) AF: 0.599 AC: 40709 AN: 67982

Other (OTH) AF: 0.629 AC: 1327 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.27
DANN	Benign	0.53
PhyloP100		-0.45

Splicing

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

Other links and lift over

dbSNP: rs1251078; hg19: chr1-76189488;