chr1-75640990-T-C

Variant names:

• chr1-75640990-T-C
• rs211718
• XM_017000609.2:c.-70+1383A>G

Variant summary

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

The XM_017000609.2(SLC44A5):​c.-70+1383A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.75 in 151,860 control chromosomes in the GnomAD database, including 43,038 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 0.75 (43038 hom., cov: 31)
• Consequence: SLC44A5 XM_017000609.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 52 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]

ENSG00000293044 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC44A5	XM_017000609.2	c.-70+1383A>G		intron_variant	Intron 3 of 25		XP_016856098.1
SLC44A5	XM_017000610.2	c.-70+1383A>G		intron_variant	Intron 3 of 25		XP_016856099.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293044	ENST00000648424.1	n.*188A>G		downstream_gene_variant
ENSG00000293044	ENST00000746220.1	n.*188A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.750 AC: 113786 AN: 151742 Hom.: 42999 Cov.: 31

Gnomad AFR AF: 0.823

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.705

Gnomad ASJ AF: 0.790

Gnomad EAS AF: 0.959

Gnomad SAS AF: 0.807

Gnomad FIN AF: 0.738

Gnomad MID AF: 0.739

Gnomad NFE AF: 0.696

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.750 AC: 113886 AN: 151860 Hom.: 43038 Cov.: 31 AF XY: 0.754 AC XY: 55919 AN XY: 74204

African (AFR) AF: 0.823 AC: 34099 AN: 41430

American (AMR) AF: 0.705 AC: 10721 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.790 AC: 2739 AN: 3468

East Asian (EAS) AF: 0.959 AC: 4954 AN: 5164

South Asian (SAS) AF: 0.807 AC: 3889 AN: 4820

European-Finnish (FIN) AF: 0.738 AC: 7792 AN: 10556

Middle Eastern (MID) AF: 0.729 AC: 213 AN: 292

European-Non Finnish (NFE) AF: 0.696 AC: 47285 AN: 67902

Other (OTH) AF: 0.743 AC: 1563 AN: 2104

Alfa AF: 0.719 Hom.: 175784

Bravo AF: 0.751

Asia WGS AF: 0.829 AC: 2879 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.52
DANN	Benign	0.36
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs211718; hg19: chr1-76106675;