rs211718

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:):

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	UniProt
SLC44A5	XM_017000609.2	c.-70+1383A>G		intron_variant
SLC44A5	XM_017000610.2	c.-70+1383A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;