chr7-41708910-C-T

Position:

• chr7-41708910-C-T

Variant summary

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

The ENST00000686185.1(ENSG00000289403):​n.142G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 152,072 control chromosomes in the GnomAD database, including 3,220 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 0.19 (3220 hom., cov: 33)
• Consequence: ENST00000686185.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.884

Genes affected

(HGNC:):

INHBA-AS1 (HGNC:40303): (INHBA antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.242 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
INHBA-AS1	NR_027118.2	n.171-1688C>T		intron_variant, non_coding_transcript_variant
INHBA-AS1	NR_027119.2	n.171-1688C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000686185.1	n.142G>A		non_coding_transcript_exon_variant	1/2
INHBA-AS1	ENST00000415848.6	n.174-1688C>T		intron_variant, non_coding_transcript_variant		1

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28586 AN: 151954 Hom.: 3221 Cov.: 33

Gnomad AFR AF: 0.0632

Gnomad AMI AF: 0.274

Gnomad AMR AF: 0.178

Gnomad ASJ AF: 0.176

Gnomad EAS AF: 0.243

Gnomad SAS AF: 0.237

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.180

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.188

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

GnomAD4 genome AF: 0.188 AC: 28577 AN: 152072 Hom.: 3220 Cov.: 33 AF XY: 0.189 AC XY: 14058 AN XY: 74328

Gnomad4 AFR AF: 0.0631

Gnomad4 AMR AF: 0.178

Gnomad4 ASJ AF: 0.176

Gnomad4 EAS AF: 0.243

Gnomad4 SAS AF: 0.236

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.185

Alfa AF: 0.181 Hom.: 953

Bravo AF: 0.174

Asia WGS AF: 0.195 AC: 675 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.30
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1122291; hg19: chr7-41748508;