7-110407907-C-T

Position:

• chr7-110407907-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000667232.1(ENSG00000226965):​n.411+24904G>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.42 in 151,814 control chromosomes in the GnomAD database, including 13,718 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 0.42 (13718 hom., cov: 32)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.563

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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 = 0.45 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.386+24904G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667232.1	n.411+24904G>A		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.331-42617G>A		intron_variant, non_coding_transcript_variant
	ENST00000666128.1	n.97+24904G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.420 AC: 63752 AN: 151696 Hom.: 13712 Cov.: 32

Gnomad AFR AF: 0.456

Gnomad AMI AF: 0.367

Gnomad AMR AF: 0.422

Gnomad ASJ AF: 0.403

Gnomad EAS AF: 0.175

Gnomad SAS AF: 0.239

Gnomad FIN AF: 0.545

Gnomad MID AF: 0.389

Gnomad NFE AF: 0.412

Gnomad OTH AF: 0.417

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

GnomAD4 genome AF: 0.420 AC: 63787 AN: 151814 Hom.: 13718 Cov.: 32 AF XY: 0.419 AC XY: 31105 AN XY: 74168

Gnomad4 AFR AF: 0.456

Gnomad4 AMR AF: 0.421

Gnomad4 ASJ AF: 0.403

Gnomad4 EAS AF: 0.175

Gnomad4 SAS AF: 0.240

Gnomad4 FIN AF: 0.545

Gnomad4 NFE AF: 0.412

Gnomad4 OTH AF: 0.412

Alfa AF: 0.398 Hom.: 18871

Bravo AF: 0.414

Asia WGS AF: 0.212 AC: 742 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.85
CADD	Benign	8.5
DANN	Benign	0.84

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4730430; hg19: chr7-110047964;