7-110407414-C-T

Position:

• chr7-110407414-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+25397G>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 0.449 in 151,748 control chromosomes in the GnomAD database, including 15,512 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 0.45 (15512 hom., cov: 31)
• Consequence: ENST00000667232.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.324

Genes affected

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.61 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105375451	XR_927863.3	n.386+25397G>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
	ENST00000667232.1	n.411+25397G>A		intron_variant, non_coding_transcript_variant
	ENST00000658032.1	n.331-42124G>A		intron_variant, non_coding_transcript_variant
	ENST00000666128.1	n.97+25397G>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.449 AC: 68123 AN: 151628 Hom.: 15485 Cov.: 31

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.511

Gnomad AMR AF: 0.451

Gnomad ASJ AF: 0.411

Gnomad EAS AF: 0.627

Gnomad SAS AF: 0.568

Gnomad FIN AF: 0.362

Gnomad MID AF: 0.484

Gnomad NFE AF: 0.437

Gnomad OTH AF: 0.450

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

GnomAD4 genome AF: 0.449 AC: 68196 AN: 151748 Hom.: 15512 Cov.: 31 AF XY: 0.451 AC XY: 33415 AN XY: 74128

Gnomad4 AFR AF: 0.457

Gnomad4 AMR AF: 0.451

Gnomad4 ASJ AF: 0.411

Gnomad4 EAS AF: 0.628

Gnomad4 SAS AF: 0.568

Gnomad4 FIN AF: 0.362

Gnomad4 NFE AF: 0.437

Gnomad4 OTH AF: 0.454

Alfa AF: 0.444 Hom.: 20501

Bravo AF: 0.457

Asia WGS AF: 0.604 AC: 2085 AN: 3462

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	1.3
DANN	Benign	0.72

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6968385; hg19: chr7-110047471;