chr7-103469002-T-A

Variant names:

• chr7-103469002-T-A
• rs1978198
• ENST00000422488.1:n.1365+22334T>A

Variant summary

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

The ENST00000422488.1(SLC26A5-AS1):​n.1365+22334T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.445 in 152,150 control chromosomes in the GnomAD database, including 17,049 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 0.44 (17049 hom., cov: 32)
• Consequence: SLC26A5-AS1 ENST00000422488.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.621
• Publications: 3 publications found

Genes affected

SLC26A5-AS1 (HGNC:55680): (SLC26A5 antisense RNA 1)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.686 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SLC26A5-AS1	NR_110141.1	n.1365+22334T>A		intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SLC26A5-AS1	ENST00000422488.1	n.1365+22334T>A		intron_variant	Intron 2 of 3	1
SLC26A5-AS1	ENST00000660729.1	n.307+22334T>A		intron_variant	Intron 2 of 2
SLC26A5-AS1	ENST00000841470.1	n.292+22334T>A		intron_variant	Intron 2 of 2
SLC26A5-AS1	ENST00000841471.1	n.305-21176T>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.444 AC: 67527 AN: 152032 Hom.: 16998 Cov.: 32

Gnomad AFR AF: 0.692

Gnomad AMI AF: 0.282

Gnomad AMR AF: 0.366

Gnomad ASJ AF: 0.253

Gnomad EAS AF: 0.523

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.407

Gnomad MID AF: 0.282

Gnomad NFE AF: 0.324

Gnomad OTH AF: 0.403

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

GnomAD4 genome AF: 0.445 AC: 67643 AN: 152150 Hom.: 17049 Cov.: 32 AF XY: 0.450 AC XY: 33485 AN XY: 74386

African (AFR) AF: 0.693 AC: 28746 AN: 41510

American (AMR) AF: 0.366 AC: 5597 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.253 AC: 877 AN: 3470

East Asian (EAS) AF: 0.522 AC: 2706 AN: 5182

South Asian (SAS) AF: 0.453 AC: 2186 AN: 4824

European-Finnish (FIN) AF: 0.407 AC: 4298 AN: 10568

Middle Eastern (MID) AF: 0.276 AC: 81 AN: 294

European-Non Finnish (NFE) AF: 0.324 AC: 22033 AN: 67986

Other (OTH) AF: 0.408 AC: 862 AN: 2114

Alfa AF: 0.402 Hom.: 1701

Bravo AF: 0.448

Asia WGS AF: 0.538 AC: 1869 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	7.2
DANN	Benign	0.61
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs1978198; hg19: chr7-103109449;