rs4144887

chr6-166334024-G-A

Variant summary

Our verdict is Benign. Variant got -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

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]

ACMG classification

Verdict is Benign. Variant got -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/exons	MANE	UniProt
SFT2D1	NM_145169.3	c.64-3777C>T		intron_variant		ENST00000361731.4
SFT2D1	NR_130112.2	n.128-2617C>T		intron_variant, non_coding_transcript_variant
SFT2D1	NR_130113.2	n.128-2617C>T		intron_variant, non_coding_transcript_variant
SFT2D1	NR_130114.2	n.128-2626C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SFT2D1	ENST00000361731.4	c.64-3777C>T		intron_variant		1	NM_145169.3	P1
SFT2D1	ENST00000487841.5	n.130-2617C>T		intron_variant, non_coding_transcript_variant		1
SFT2D1	ENST00000478705.5	n.159-2617C>T		intron_variant, non_coding_transcript_variant		2

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

Gnomad4 AFR AF: 0.361

Gnomad4 AMR AF: 0.240

Gnomad4 ASJ AF: 0.272

Gnomad4 EAS AF: 0.342

Gnomad4 SAS AF: 0.254

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.274

Alfa AF: 0.249 Hom.: 770

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

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

Other links and lift over

dbSNP: rs4144887; hg19: chr6-166747512;