1-75717044-T-C

Position:

• chr1-75717044-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.-190+3305A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 147,824 control chromosomes in the GnomAD database, including 2,675 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 0.12 (2675 hom., cov: 31)
• Consequence: SLC44A5 XM_017000609.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169

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]

ENSG00000230863 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.356 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A5	XM_017000609.2	c.-190+3305A>G		intron_variant			XP_016856098.1
SLC44A5	XM_017000610.2	c.-190+3305A>G		intron_variant			XP_016856099.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000230863	ENST00000433521.2	n.248+3305A>G		intron_variant		3
ENSG00000230863	ENST00000648424.1	n.165+3305A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18085 AN: 147708 Hom.: 2663 Cov.: 31

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.0102

Gnomad AMR AF: 0.0639

Gnomad ASJ AF: 0.00498

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00851

Gnomad FIN AF: 0.0252

Gnomad MID AF: 0.0340

Gnomad NFE AF: 0.0310

Gnomad OTH AF: 0.0987

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

GnomAD4 genome AF: 0.123 AC: 18140 AN: 147824 Hom.: 2675 Cov.: 31 AF XY: 0.120 AC XY: 8611 AN XY: 72034

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.0637

Gnomad4 ASJ AF: 0.00498

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00831

Gnomad4 FIN AF: 0.0252

Gnomad4 NFE AF: 0.0310

Gnomad4 OTH AF: 0.0977

Alfa AF: 0.0101 Hom.: 4

Bravo AF: 0.133

Asia WGS AF: 0.0280 AC: 99 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	5.5
DANN	Benign	0.79

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs815311; hg19: chr1-76182729;