7-9926280-C-T

Variant names:

• chr7-9926280-C-T
• rs1557978
• ENST00000663710.1:n.62-35005C>T

Variant summary

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

The ENST00000663710.1(ENSG00000235431):​n.62-35005C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.29 in 151,774 control chromosomes in the GnomAD database, including 6,746 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 0.29 (6746 hom., cov: 32)
• Consequence: ENSG00000235431 ENST00000663710.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.149
• Publications: 4 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.336 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000663710.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000235431	ENST00000663710.1		n.62-35005C>T		intron	N/A
	ENSG00000295572	ENST00000731005.1		n.150+33963G>A		intron	N/A
	ENSG00000295572	ENST00000731006.1		n.41+3196G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.290 AC: 44047 AN: 151654 Hom.: 6741 Cov.: 32

Gnomad AFR AF: 0.192

Gnomad AMI AF: 0.296

Gnomad AMR AF: 0.303

Gnomad ASJ AF: 0.314

Gnomad EAS AF: 0.260

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.341

Gnomad MID AF: 0.244

Gnomad NFE AF: 0.340

Gnomad OTH AF: 0.283

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

GnomAD4 genome AF: 0.290 AC: 44068 AN: 151774 Hom.: 6746 Cov.: 32 AF XY: 0.289 AC XY: 21470 AN XY: 74170

African (AFR) AF: 0.192 AC: 7967 AN: 41462

American (AMR) AF: 0.303 AC: 4598 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.314 AC: 1087 AN: 3466

East Asian (EAS) AF: 0.260 AC: 1345 AN: 5166

South Asian (SAS) AF: 0.307 AC: 1477 AN: 4814

European-Finnish (FIN) AF: 0.341 AC: 3603 AN: 10552

Middle Eastern (MID) AF: 0.238 AC: 70 AN: 294

European-Non Finnish (NFE) AF: 0.340 AC: 23061 AN: 67808

Other (OTH) AF: 0.280 AC: 591 AN: 2108

Alfa AF: 0.313 Hom.: 25444

Bravo AF: 0.282

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.30
PhyloP100		-0.15

Splicing

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

Other links and lift over

dbSNP: rs1557978; hg19: chr7-9965912;