7-127651487-T-TAA

Variant names:

• chr7-127651487-T-TAA
• rs2308067
• ENST00000691038.3:n.581_582insTT

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BA1

The ENST00000691038.3(SND1-DT):​n.581_582insTT variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.73 (41477 hom., cov: 0)
• Consequence: SND1-DT ENST00000691038.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.429
• Publications: 3 publications found

Genes affected

SND1-DT (HGNC:55639): (SND1 divergent transcript)

ACMG classification

Our verdict: Benign. The variant received -8 ACMG points.

• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.909 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SND1-DT	NR_186577.1	n.160+185_160+186insTT		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SND1-DT	ENST00000691038.3	n.581_582insTT		non_coding_transcript_exon_variant	Exon 1 of 1
SND1-DT	ENST00000836785.1	n.410_411insTT		non_coding_transcript_exon_variant	Exon 1 of 2
SND1-DT	ENST00000490314.1	n.340+185_340+186insTT		intron_variant	Intron 1 of 2	4

Frequencies

GnomAD3 genomes AF: 0.726 AC: 110124 AN: 151676 Hom.: 41431 Cov.: 0

Gnomad AFR AF: 0.917

Gnomad AMI AF: 0.760

Gnomad AMR AF: 0.723

Gnomad ASJ AF: 0.786

Gnomad EAS AF: 0.308

Gnomad SAS AF: 0.609

Gnomad FIN AF: 0.609

Gnomad MID AF: 0.772

Gnomad NFE AF: 0.665

Gnomad OTH AF: 0.723

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

GnomAD4 genome AF: 0.726 AC: 110224 AN: 151792 Hom.: 41477 Cov.: 0 AF XY: 0.718 AC XY: 53222 AN XY: 74154

African (AFR) AF: 0.917 AC: 37985 AN: 41430

American (AMR) AF: 0.722 AC: 11032 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.786 AC: 2728 AN: 3470

East Asian (EAS) AF: 0.308 AC: 1582 AN: 5142

South Asian (SAS) AF: 0.607 AC: 2923 AN: 4812

European-Finnish (FIN) AF: 0.609 AC: 6377 AN: 10476

Middle Eastern (MID) AF: 0.769 AC: 226 AN: 294

European-Non Finnish (NFE) AF: 0.665 AC: 45162 AN: 67886

Other (OTH) AF: 0.723 AC: 1522 AN: 2106

Alfa AF: 0.685 Hom.: 4486

Bravo AF: 0.744

Asia WGS AF: 0.509 AC: 1772 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.43
Mutation Taster		=71/29	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs2308067; hg19: chr7-127291541;