rs4144887

Variant names:

• chr6-166334024-G-A
• rs4144887
• NM_145169.3:c.64-3777C>T

Variant summary

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

The NM_145169.3(SFT2D1):​c.64-3777C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.27 in 152,142 control chromosomes in the GnomAD database, including 5,896 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 0.27 (5896 hom., cov: 33)
• Consequence: SFT2D1 NM_145169.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.82
• Publications: 4 publications found

Genes affected

SFT2D1 (HGNC:21102): (SFT2 domain containing 1) Predicted to be involved in protein transport and vesicle-mediated transport. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

ENSG00000308813 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• 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
SFT2D1	NM_145169.3	c.64-3777C>T		intron_variant	Intron 1 of 7	ENST00000361731.4	NP_660152.1
SFT2D1	NR_130112.2	n.128-2617C>T		intron_variant	Intron 1 of 8
SFT2D1	NR_130113.2	n.128-2617C>T		intron_variant	Intron 1 of 6
SFT2D1	NR_130114.2	n.128-2626C>T		intron_variant	Intron 1 of 6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SFT2D1	ENST00000361731.4	c.64-3777C>T		intron_variant	Intron 1 of 7	1	NM_145169.3	ENSP00000354590.3
SFT2D1	ENST00000487841.5	n.130-2617C>T		intron_variant	Intron 1 of 7	1
SFT2D1	ENST00000478705.5	n.159-2617C>T		intron_variant	Intron 1 of 8	2
ENSG00000308813	ENST00000836544.1	n.245-1979C>T		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.270 AC: 40994 AN: 152024 Hom.: 5888 Cov.: 33

Gnomad AFR AF: 0.361

Gnomad AMI AF: 0.221

Gnomad AMR AF: 0.240

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.342

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.307

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.274

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

GnomAD4 genome AF: 0.270 AC: 41034 AN: 152142 Hom.: 5896 Cov.: 33 AF XY: 0.269 AC XY: 19989 AN XY: 74360

African (AFR) AF: 0.361 AC: 14988 AN: 41482

American (AMR) AF: 0.240 AC: 3662 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 943 AN: 3470

East Asian (EAS) AF: 0.342 AC: 1771 AN: 5180

South Asian (SAS) AF: 0.254 AC: 1223 AN: 4816

European-Finnish (FIN) AF: 0.186 AC: 1972 AN: 10584

Middle Eastern (MID) AF: 0.303 AC: 89 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15606 AN: 68000

Other (OTH) AF: 0.274 AC: 579 AN: 2116

Alfa AF: 0.253 Hom.: 817

Bravo AF: 0.276

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	4.8
DANN	Benign	0.72
PhyloP100		1.8
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs4144887; hg19: chr6-166747512;