rs6978190

Variant names:

• chr7-9958907-T-C
• rs6978190
• ENST00000663710.1:n.62-2378T>C

Variant summary

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

The ENST00000663710.1(ENSG00000235431):​n.62-2378T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0741 in 152,218 control chromosomes in the GnomAD database, including 1,195 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 0.074 (1195 hom., cov: 33)
• Consequence: ENSG00000235431 ENST00000663710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.617
• Publications: 0 publications found

Genes affected

ENSG00000235431 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.85).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.232 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000235431	ENST00000663710.1	n.62-2378T>C		intron_variant	Intron 1 of 4
ENSG00000295572	ENST00000731005.1	n.150+1336A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.0740 AC: 11250 AN: 152100 Hom.: 1192 Cov.: 33

Gnomad AFR AF: 0.236

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0331

Gnomad ASJ AF: 0.0418

Gnomad EAS AF: 0.0503

Gnomad SAS AF: 0.0459

Gnomad FIN AF: 0.000188

Gnomad MID AF: 0.0538

Gnomad NFE AF: 0.00310

Gnomad OTH AF: 0.0584

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

GnomAD4 genome AF: 0.0741 AC: 11284 AN: 152218 Hom.: 1195 Cov.: 33 AF XY: 0.0723 AC XY: 5382 AN XY: 74438

African (AFR) AF: 0.236 AC: 9797 AN: 41470

American (AMR) AF: 0.0331 AC: 506 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0418 AC: 145 AN: 3472

East Asian (EAS) AF: 0.0502 AC: 260 AN: 5182

South Asian (SAS) AF: 0.0457 AC: 221 AN: 4832

European-Finnish (FIN) AF: 0.000188 AC: 2 AN: 10624

Middle Eastern (MID) AF: 0.0578 AC: 17 AN: 294

European-Non Finnish (NFE) AF: 0.00310 AC: 211 AN: 68028

Other (OTH) AF: 0.0592 AC: 125 AN: 2112

Alfa AF: 0.0512 Hom.: 125

Bravo AF: 0.0849

Asia WGS AF: 0.0560 AC: 196 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	2.9
DANN	Benign	0.87
PhyloP100		0.62

Splicing

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

Other links and lift over

dbSNP: rs6978190; hg19: chr7-9998534;