Variant chr1-75304940-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001130058.2(SLC44A5):c.102-4255G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.588 in 151,946 control chromosomes in the GnomAD database, including 26,690 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 0.59 ( 26690 hom., cov: 32)

Consequence

SLC44A5
NM_001130058.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.637

Variant links:

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]

SLC44A5 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.827 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SLC44A5	NM_001130058.2 linkuse as main transcript	c.102-4255G>A		intron_variant		ENST00000370859.8	NP_001123530.1

Ensembl

Gene	Transcript	HGVSc	Effect	TSL	MANE	Protein	Appris	UniProt
SLC44A5	ENST00000370859.8 linkuse as main transcript	c.102-4255G>A	intron_variant	2	NM_001130058.2	ENSP00000359896	A1	Q8NCS7-4
SLC44A5	ENST00000370855.5 linkuse as main transcript	c.102-4255G>A	intron_variant	1		ENSP00000359892	P4	Q8NCS7-1
SLC44A5	ENST00000469525.1 linkuse as main transcript	n.386-4255G>A	intron_variant, non_coding_transcript_variant	5

Frequencies

GnomAD3 genomes

AF:

0.588

AC:

89265

AN:

151828

Hom.:

26671

Cov.:

show subpopulations

Gnomad AFR

AF:

0.621

Gnomad AMI

AF:

0.522

Gnomad AMR

AF:

0.653

Gnomad ASJ

AF:

0.549

Gnomad EAS

AF:

0.849

Gnomad SAS

AF:

0.489

Gnomad FIN

AF:

0.624

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.537

Gnomad OTH

AF:

0.616

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

GnomAD4 genome

AF:

0.588

AC:

89338

AN:

151946

Hom.:

26690

Cov.:

AF XY:

0.595

AC XY:

44200

AN XY:

74290

show subpopulations

Gnomad4 AFR

AF:

0.621

Gnomad4 AMR

AF:

0.653

Gnomad4 ASJ

AF:

0.549

Gnomad4 EAS

AF:

0.848

Gnomad4 SAS

AF:

0.488

Gnomad4 FIN

AF:

0.624

Gnomad4 NFE

AF:

0.537

Gnomad4 OTH

AF:

0.614

Alfa

AF:

0.551

Hom.:

30169

Bravo

AF:

0.597

Asia WGS

AF:

0.634

AC:

2206

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.97

CADD

Benign

DANN

Benign

0.71

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over