1-75717044-T-C

Variant names:

• chr1-75717044-T-C
• rs815311
• ENST00000433521.2:n.248+3305A>G

Variant summary

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

The ENST00000433521.2(ENSG00000293044):​n.248+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: ENSG00000293044 ENST00000433521.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.169
• Publications: 2 publications found

Genes affected

ENSG00000293044 (HGNC:):

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]

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SLC44A5	XM_017000609.2	c.-190+3305A>G		intron_variant	Intron 2 of 25		XP_016856098.1
SLC44A5	XM_017000610.2	c.-190+3305A>G		intron_variant	Intron 2 of 25		XP_016856099.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000293044	ENST00000433521.2	n.248+3305A>G		intron_variant	Intron 3 of 3	3
ENSG00000293044	ENST00000648424.1	n.165+3305A>G		intron_variant	Intron 2 of 2
ENSG00000293044	ENST00000746220.1	n.529+3305A>G		intron_variant	Intron 3 of 5

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

African (AFR) AF: 0.360 AC: 14617 AN: 40548

American (AMR) AF: 0.0637 AC: 937 AN: 14718

Ashkenazi Jewish (ASJ) AF: 0.00498 AC: 17 AN: 3416

East Asian (EAS) AF: 0.00 AC: 0 AN: 4970

South Asian (SAS) AF: 0.00831 AC: 38 AN: 4574

European-Finnish (FIN) AF: 0.0252 AC: 249 AN: 9866

Middle Eastern (MID) AF: 0.0362 AC: 10 AN: 276

European-Non Finnish (NFE) AF: 0.0310 AC: 2061 AN: 66506

Other (OTH) AF: 0.0977 AC: 202 AN: 2068

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
PhyloP100		0.17

Splicing

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

Other links and lift over

dbSNP: rs815311; hg19: chr1-76182729;