chr1-75640990-T-C

Position:

• chr1-75640990-T-C

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	Protein	UniProt
SLC44A5	XM_017000609.2	c.-70+1383A>G		intron_variant			XP_016856098.1
SLC44A5	XM_017000610.2	c.-70+1383A>G		intron_variant			XP_016856099.1
		n.75640990T>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.823

Gnomad4 AMR AF: 0.705

Gnomad4 ASJ AF: 0.790

Gnomad4 EAS AF: 0.959

Gnomad4 SAS AF: 0.807

Gnomad4 FIN AF: 0.738

Gnomad4 NFE AF: 0.696

Gnomad4 OTH AF: 0.743

Alfa AF: 0.714 Hom.: 79622

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs211718; hg19: chr1-76106675;